1: /* $Id: imach.c,v 1.159 2014/09/01 10:34:10 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.159 2014/09/01 10:34:10 brouard
5: Summary: WIN32
6: Author: Brouard
7:
8: Revision 1.158 2014/08/27 17:11:51 brouard
9: *** empty log message ***
10:
11: Revision 1.157 2014/08/27 16:26:55 brouard
12: Summary: Preparing windows Visual studio version
13: Author: Brouard
14:
15: In order to compile on Visual studio, time.h is now correct and time_t
16: and tm struct should be used. difftime should be used but sometimes I
17: just make the differences in raw time format (time(&now).
18: Trying to suppress #ifdef LINUX
19: Add xdg-open for __linux in order to open default browser.
20:
21: Revision 1.156 2014/08/25 20:10:10 brouard
22: *** empty log message ***
23:
24: Revision 1.155 2014/08/25 18:32:34 brouard
25: Summary: New compile, minor changes
26: Author: Brouard
27:
28: Revision 1.154 2014/06/20 17:32:08 brouard
29: Summary: Outputs now all graphs of convergence to period prevalence
30:
31: Revision 1.153 2014/06/20 16:45:46 brouard
32: Summary: If 3 live state, convergence to period prevalence on same graph
33: Author: Brouard
34:
35: Revision 1.152 2014/06/18 17:54:09 brouard
36: Summary: open browser, use gnuplot on same dir than imach if not found in the path
37:
38: Revision 1.151 2014/06/18 16:43:30 brouard
39: *** empty log message ***
40:
41: Revision 1.150 2014/06/18 16:42:35 brouard
42: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
43: Author: brouard
44:
45: Revision 1.149 2014/06/18 15:51:14 brouard
46: Summary: Some fixes in parameter files errors
47: Author: Nicolas Brouard
48:
49: Revision 1.148 2014/06/17 17:38:48 brouard
50: Summary: Nothing new
51: Author: Brouard
52:
53: Just a new packaging for OS/X version 0.98nS
54:
55: Revision 1.147 2014/06/16 10:33:11 brouard
56: *** empty log message ***
57:
58: Revision 1.146 2014/06/16 10:20:28 brouard
59: Summary: Merge
60: Author: Brouard
61:
62: Merge, before building revised version.
63:
64: Revision 1.145 2014/06/10 21:23:15 brouard
65: Summary: Debugging with valgrind
66: Author: Nicolas Brouard
67:
68: Lot of changes in order to output the results with some covariates
69: After the Edimburgh REVES conference 2014, it seems mandatory to
70: improve the code.
71: No more memory valgrind error but a lot has to be done in order to
72: continue the work of splitting the code into subroutines.
73: Also, decodemodel has been improved. Tricode is still not
74: optimal. nbcode should be improved. Documentation has been added in
75: the source code.
76:
77: Revision 1.143 2014/01/26 09:45:38 brouard
78: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
79:
80: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
81: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
82:
83: Revision 1.142 2014/01/26 03:57:36 brouard
84: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
85:
86: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
87:
88: Revision 1.141 2014/01/26 02:42:01 brouard
89: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
90:
91: Revision 1.140 2011/09/02 10:37:54 brouard
92: Summary: times.h is ok with mingw32 now.
93:
94: Revision 1.139 2010/06/14 07:50:17 brouard
95: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
96: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
97:
98: Revision 1.138 2010/04/30 18:19:40 brouard
99: *** empty log message ***
100:
101: Revision 1.137 2010/04/29 18:11:38 brouard
102: (Module): Checking covariates for more complex models
103: than V1+V2. A lot of change to be done. Unstable.
104:
105: Revision 1.136 2010/04/26 20:30:53 brouard
106: (Module): merging some libgsl code. Fixing computation
107: of likelione (using inter/intrapolation if mle = 0) in order to
108: get same likelihood as if mle=1.
109: Some cleaning of code and comments added.
110:
111: Revision 1.135 2009/10/29 15:33:14 brouard
112: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
113:
114: Revision 1.134 2009/10/29 13:18:53 brouard
115: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
116:
117: Revision 1.133 2009/07/06 10:21:25 brouard
118: just nforces
119:
120: Revision 1.132 2009/07/06 08:22:05 brouard
121: Many tings
122:
123: Revision 1.131 2009/06/20 16:22:47 brouard
124: Some dimensions resccaled
125:
126: Revision 1.130 2009/05/26 06:44:34 brouard
127: (Module): Max Covariate is now set to 20 instead of 8. A
128: lot of cleaning with variables initialized to 0. Trying to make
129: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
130:
131: Revision 1.129 2007/08/31 13:49:27 lievre
132: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
133:
134: Revision 1.128 2006/06/30 13:02:05 brouard
135: (Module): Clarifications on computing e.j
136:
137: Revision 1.127 2006/04/28 18:11:50 brouard
138: (Module): Yes the sum of survivors was wrong since
139: imach-114 because nhstepm was no more computed in the age
140: loop. Now we define nhstepma in the age loop.
141: (Module): In order to speed up (in case of numerous covariates) we
142: compute health expectancies (without variances) in a first step
143: and then all the health expectancies with variances or standard
144: deviation (needs data from the Hessian matrices) which slows the
145: computation.
146: In the future we should be able to stop the program is only health
147: expectancies and graph are needed without standard deviations.
148:
149: Revision 1.126 2006/04/28 17:23:28 brouard
150: (Module): Yes the sum of survivors was wrong since
151: imach-114 because nhstepm was no more computed in the age
152: loop. Now we define nhstepma in the age loop.
153: Version 0.98h
154:
155: Revision 1.125 2006/04/04 15:20:31 lievre
156: Errors in calculation of health expectancies. Age was not initialized.
157: Forecasting file added.
158:
159: Revision 1.124 2006/03/22 17:13:53 lievre
160: Parameters are printed with %lf instead of %f (more numbers after the comma).
161: The log-likelihood is printed in the log file
162:
163: Revision 1.123 2006/03/20 10:52:43 brouard
164: * imach.c (Module): <title> changed, corresponds to .htm file
165: name. <head> headers where missing.
166:
167: * imach.c (Module): Weights can have a decimal point as for
168: English (a comma might work with a correct LC_NUMERIC environment,
169: otherwise the weight is truncated).
170: Modification of warning when the covariates values are not 0 or
171: 1.
172: Version 0.98g
173:
174: Revision 1.122 2006/03/20 09:45:41 brouard
175: (Module): Weights can have a decimal point as for
176: English (a comma might work with a correct LC_NUMERIC environment,
177: otherwise the weight is truncated).
178: Modification of warning when the covariates values are not 0 or
179: 1.
180: Version 0.98g
181:
182: Revision 1.121 2006/03/16 17:45:01 lievre
183: * imach.c (Module): Comments concerning covariates added
184:
185: * imach.c (Module): refinements in the computation of lli if
186: status=-2 in order to have more reliable computation if stepm is
187: not 1 month. Version 0.98f
188:
189: Revision 1.120 2006/03/16 15:10:38 lievre
190: (Module): refinements in the computation of lli if
191: status=-2 in order to have more reliable computation if stepm is
192: not 1 month. Version 0.98f
193:
194: Revision 1.119 2006/03/15 17:42:26 brouard
195: (Module): Bug if status = -2, the loglikelihood was
196: computed as likelihood omitting the logarithm. Version O.98e
197:
198: Revision 1.118 2006/03/14 18:20:07 brouard
199: (Module): varevsij Comments added explaining the second
200: table of variances if popbased=1 .
201: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
202: (Module): Function pstamp added
203: (Module): Version 0.98d
204:
205: Revision 1.117 2006/03/14 17:16:22 brouard
206: (Module): varevsij Comments added explaining the second
207: table of variances if popbased=1 .
208: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
209: (Module): Function pstamp added
210: (Module): Version 0.98d
211:
212: Revision 1.116 2006/03/06 10:29:27 brouard
213: (Module): Variance-covariance wrong links and
214: varian-covariance of ej. is needed (Saito).
215:
216: Revision 1.115 2006/02/27 12:17:45 brouard
217: (Module): One freematrix added in mlikeli! 0.98c
218:
219: Revision 1.114 2006/02/26 12:57:58 brouard
220: (Module): Some improvements in processing parameter
221: filename with strsep.
222:
223: Revision 1.113 2006/02/24 14:20:24 brouard
224: (Module): Memory leaks checks with valgrind and:
225: datafile was not closed, some imatrix were not freed and on matrix
226: allocation too.
227:
228: Revision 1.112 2006/01/30 09:55:26 brouard
229: (Module): Back to gnuplot.exe instead of wgnuplot.exe
230:
231: Revision 1.111 2006/01/25 20:38:18 brouard
232: (Module): Lots of cleaning and bugs added (Gompertz)
233: (Module): Comments can be added in data file. Missing date values
234: can be a simple dot '.'.
235:
236: Revision 1.110 2006/01/25 00:51:50 brouard
237: (Module): Lots of cleaning and bugs added (Gompertz)
238:
239: Revision 1.109 2006/01/24 19:37:15 brouard
240: (Module): Comments (lines starting with a #) are allowed in data.
241:
242: Revision 1.108 2006/01/19 18:05:42 lievre
243: Gnuplot problem appeared...
244: To be fixed
245:
246: Revision 1.107 2006/01/19 16:20:37 brouard
247: Test existence of gnuplot in imach path
248:
249: Revision 1.106 2006/01/19 13:24:36 brouard
250: Some cleaning and links added in html output
251:
252: Revision 1.105 2006/01/05 20:23:19 lievre
253: *** empty log message ***
254:
255: Revision 1.104 2005/09/30 16:11:43 lievre
256: (Module): sump fixed, loop imx fixed, and simplifications.
257: (Module): If the status is missing at the last wave but we know
258: that the person is alive, then we can code his/her status as -2
259: (instead of missing=-1 in earlier versions) and his/her
260: contributions to the likelihood is 1 - Prob of dying from last
261: health status (= 1-p13= p11+p12 in the easiest case of somebody in
262: the healthy state at last known wave). Version is 0.98
263:
264: Revision 1.103 2005/09/30 15:54:49 lievre
265: (Module): sump fixed, loop imx fixed, and simplifications.
266:
267: Revision 1.102 2004/09/15 17:31:30 brouard
268: Add the possibility to read data file including tab characters.
269:
270: Revision 1.101 2004/09/15 10:38:38 brouard
271: Fix on curr_time
272:
273: Revision 1.100 2004/07/12 18:29:06 brouard
274: Add version for Mac OS X. Just define UNIX in Makefile
275:
276: Revision 1.99 2004/06/05 08:57:40 brouard
277: *** empty log message ***
278:
279: Revision 1.98 2004/05/16 15:05:56 brouard
280: New version 0.97 . First attempt to estimate force of mortality
281: directly from the data i.e. without the need of knowing the health
282: state at each age, but using a Gompertz model: log u =a + b*age .
283: This is the basic analysis of mortality and should be done before any
284: other analysis, in order to test if the mortality estimated from the
285: cross-longitudinal survey is different from the mortality estimated
286: from other sources like vital statistic data.
287:
288: The same imach parameter file can be used but the option for mle should be -3.
289:
290: Agnès, who wrote this part of the code, tried to keep most of the
291: former routines in order to include the new code within the former code.
292:
293: The output is very simple: only an estimate of the intercept and of
294: the slope with 95% confident intervals.
295:
296: Current limitations:
297: A) Even if you enter covariates, i.e. with the
298: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
299: B) There is no computation of Life Expectancy nor Life Table.
300:
301: Revision 1.97 2004/02/20 13:25:42 lievre
302: Version 0.96d. Population forecasting command line is (temporarily)
303: suppressed.
304:
305: Revision 1.96 2003/07/15 15:38:55 brouard
306: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
307: rewritten within the same printf. Workaround: many printfs.
308:
309: Revision 1.95 2003/07/08 07:54:34 brouard
310: * imach.c (Repository):
311: (Repository): Using imachwizard code to output a more meaningful covariance
312: matrix (cov(a12,c31) instead of numbers.
313:
314: Revision 1.94 2003/06/27 13:00:02 brouard
315: Just cleaning
316:
317: Revision 1.93 2003/06/25 16:33:55 brouard
318: (Module): On windows (cygwin) function asctime_r doesn't
319: exist so I changed back to asctime which exists.
320: (Module): Version 0.96b
321:
322: Revision 1.92 2003/06/25 16:30:45 brouard
323: (Module): On windows (cygwin) function asctime_r doesn't
324: exist so I changed back to asctime which exists.
325:
326: Revision 1.91 2003/06/25 15:30:29 brouard
327: * imach.c (Repository): Duplicated warning errors corrected.
328: (Repository): Elapsed time after each iteration is now output. It
329: helps to forecast when convergence will be reached. Elapsed time
330: is stamped in powell. We created a new html file for the graphs
331: concerning matrix of covariance. It has extension -cov.htm.
332:
333: Revision 1.90 2003/06/24 12:34:15 brouard
334: (Module): Some bugs corrected for windows. Also, when
335: mle=-1 a template is output in file "or"mypar.txt with the design
336: of the covariance matrix to be input.
337:
338: Revision 1.89 2003/06/24 12:30:52 brouard
339: (Module): Some bugs corrected for windows. Also, when
340: mle=-1 a template is output in file "or"mypar.txt with the design
341: of the covariance matrix to be input.
342:
343: Revision 1.88 2003/06/23 17:54:56 brouard
344: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
345:
346: Revision 1.87 2003/06/18 12:26:01 brouard
347: Version 0.96
348:
349: Revision 1.86 2003/06/17 20:04:08 brouard
350: (Module): Change position of html and gnuplot routines and added
351: routine fileappend.
352:
353: Revision 1.85 2003/06/17 13:12:43 brouard
354: * imach.c (Repository): Check when date of death was earlier that
355: current date of interview. It may happen when the death was just
356: prior to the death. In this case, dh was negative and likelihood
357: was wrong (infinity). We still send an "Error" but patch by
358: assuming that the date of death was just one stepm after the
359: interview.
360: (Repository): Because some people have very long ID (first column)
361: we changed int to long in num[] and we added a new lvector for
362: memory allocation. But we also truncated to 8 characters (left
363: truncation)
364: (Repository): No more line truncation errors.
365:
366: Revision 1.84 2003/06/13 21:44:43 brouard
367: * imach.c (Repository): Replace "freqsummary" at a correct
368: place. It differs from routine "prevalence" which may be called
369: many times. Probs is memory consuming and must be used with
370: parcimony.
371: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
372:
373: Revision 1.83 2003/06/10 13:39:11 lievre
374: *** empty log message ***
375:
376: Revision 1.82 2003/06/05 15:57:20 brouard
377: Add log in imach.c and fullversion number is now printed.
378:
379: */
380: /*
381: Interpolated Markov Chain
382:
383: Short summary of the programme:
384:
385: This program computes Healthy Life Expectancies from
386: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
387: first survey ("cross") where individuals from different ages are
388: interviewed on their health status or degree of disability (in the
389: case of a health survey which is our main interest) -2- at least a
390: second wave of interviews ("longitudinal") which measure each change
391: (if any) in individual health status. Health expectancies are
392: computed from the time spent in each health state according to a
393: model. More health states you consider, more time is necessary to reach the
394: Maximum Likelihood of the parameters involved in the model. The
395: simplest model is the multinomial logistic model where pij is the
396: probability to be observed in state j at the second wave
397: conditional to be observed in state i at the first wave. Therefore
398: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
399: 'age' is age and 'sex' is a covariate. If you want to have a more
400: complex model than "constant and age", you should modify the program
401: where the markup *Covariates have to be included here again* invites
402: you to do it. More covariates you add, slower the
403: convergence.
404:
405: The advantage of this computer programme, compared to a simple
406: multinomial logistic model, is clear when the delay between waves is not
407: identical for each individual. Also, if a individual missed an
408: intermediate interview, the information is lost, but taken into
409: account using an interpolation or extrapolation.
410:
411: hPijx is the probability to be observed in state i at age x+h
412: conditional to the observed state i at age x. The delay 'h' can be
413: split into an exact number (nh*stepm) of unobserved intermediate
414: states. This elementary transition (by month, quarter,
415: semester or year) is modelled as a multinomial logistic. The hPx
416: matrix is simply the matrix product of nh*stepm elementary matrices
417: and the contribution of each individual to the likelihood is simply
418: hPijx.
419:
420: Also this programme outputs the covariance matrix of the parameters but also
421: of the life expectancies. It also computes the period (stable) prevalence.
422:
423: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
424: Institut national d'études démographiques, Paris.
425: This software have been partly granted by Euro-REVES, a concerted action
426: from the European Union.
427: It is copyrighted identically to a GNU software product, ie programme and
428: software can be distributed freely for non commercial use. Latest version
429: can be accessed at http://euroreves.ined.fr/imach .
430:
431: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
432: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
433:
434: **********************************************************************/
435: /*
436: main
437: read parameterfile
438: read datafile
439: concatwav
440: freqsummary
441: if (mle >= 1)
442: mlikeli
443: print results files
444: if mle==1
445: computes hessian
446: read end of parameter file: agemin, agemax, bage, fage, estepm
447: begin-prev-date,...
448: open gnuplot file
449: open html file
450: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
451: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
452: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
453: freexexit2 possible for memory heap.
454:
455: h Pij x | pij_nom ficrestpij
456: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
457: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
458: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
459:
460: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
461: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
462: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
463: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
464: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
465:
466: forecasting if prevfcast==1 prevforecast call prevalence()
467: health expectancies
468: Variance-covariance of DFLE
469: prevalence()
470: movingaverage()
471: varevsij()
472: if popbased==1 varevsij(,popbased)
473: total life expectancies
474: Variance of period (stable) prevalence
475: end
476: */
477:
478:
479:
480:
481: #include <math.h>
482: #include <stdio.h>
483: #include <stdlib.h>
484: #include <string.h>
485:
486: #ifdef _WIN32
487: #include <io.h>
488: #else
489: #include <unistd.h>
490: #endif
491:
492: #include <limits.h>
493: #include <sys/types.h>
494: #include <sys/stat.h>
495: #include <errno.h>
496: /* extern int errno; */
497:
498: /* #ifdef LINUX */
499: /* #include <time.h> */
500: /* #include "timeval.h" */
501: /* #else */
502: /* #include <sys/time.h> */
503: /* #endif */
504:
505: #include <time.h>
506:
507: #ifdef GSL
508: #include <gsl/gsl_errno.h>
509: #include <gsl/gsl_multimin.h>
510: #endif
511:
512: /* #include <libintl.h> */
513: /* #define _(String) gettext (String) */
514:
515: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
516:
517: #define GNUPLOTPROGRAM "gnuplot"
518: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
519: #define FILENAMELENGTH 132
520:
521: #define GLOCK_ERROR_NOPATH -1 /* empty path */
522: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
523:
524: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
525: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
526:
527: #define NINTERVMAX 8
528: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
529: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
530: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
531: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
532: #define MAXN 20000
533: #define YEARM 12. /**< Number of months per year */
534: #define AGESUP 130
535: #define AGEBASE 40
536: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
537: #ifdef _WIN32
538: #define DIRSEPARATOR '\\'
539: #define CHARSEPARATOR "\\"
540: #define ODIRSEPARATOR '/'
541: #else
542: #define DIRSEPARATOR '/'
543: #define CHARSEPARATOR "/"
544: #define ODIRSEPARATOR '\\'
545: #endif
546:
547: /* $Id: imach.c,v 1.159 2014/09/01 10:34:10 brouard Exp $ */
548: /* $State: Exp $ */
549:
550: char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
551: char fullversion[]="$Revision: 1.159 $ $Date: 2014/09/01 10:34:10 $";
552: char strstart[80];
553: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
554: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
555: int nvar=0, nforce=0; /* Number of variables, number of forces */
556: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
557: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
558: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
559: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
560: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
561: int cptcovprodnoage=0; /**< Number of covariate products without age */
562: int cptcoveff=0; /* Total number of covariates to vary for printing results */
563: int cptcov=0; /* Working variable */
564: int npar=NPARMAX;
565: int nlstate=2; /* Number of live states */
566: int ndeath=1; /* Number of dead states */
567: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
568: int popbased=0;
569:
570: int *wav; /* Number of waves for this individuual 0 is possible */
571: int maxwav=0; /* Maxim number of waves */
572: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
573: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
574: int gipmx=0, gsw=0; /* Global variables on the number of contributions
575: to the likelihood and the sum of weights (done by funcone)*/
576: int mle=1, weightopt=0;
577: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
578: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
579: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
580: * wave mi and wave mi+1 is not an exact multiple of stepm. */
581: double jmean=1; /* Mean space between 2 waves */
582: double **matprod2(); /* test */
583: double **oldm, **newm, **savm; /* Working pointers to matrices */
584: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
585: /*FILE *fic ; */ /* Used in readdata only */
586: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
587: FILE *ficlog, *ficrespow;
588: int globpr=0; /* Global variable for printing or not */
589: double fretone; /* Only one call to likelihood */
590: long ipmx=0; /* Number of contributions */
591: double sw; /* Sum of weights */
592: char filerespow[FILENAMELENGTH];
593: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
594: FILE *ficresilk;
595: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
596: FILE *ficresprobmorprev;
597: FILE *fichtm, *fichtmcov; /* Html File */
598: FILE *ficreseij;
599: char filerese[FILENAMELENGTH];
600: FILE *ficresstdeij;
601: char fileresstde[FILENAMELENGTH];
602: FILE *ficrescveij;
603: char filerescve[FILENAMELENGTH];
604: FILE *ficresvij;
605: char fileresv[FILENAMELENGTH];
606: FILE *ficresvpl;
607: char fileresvpl[FILENAMELENGTH];
608: char title[MAXLINE];
609: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
610: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
611: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
612: char command[FILENAMELENGTH];
613: int outcmd=0;
614:
615: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
616:
617: char filelog[FILENAMELENGTH]; /* Log file */
618: char filerest[FILENAMELENGTH];
619: char fileregp[FILENAMELENGTH];
620: char popfile[FILENAMELENGTH];
621:
622: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
623:
624: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
625: /* struct timezone tzp; */
626: /* extern int gettimeofday(); */
627: struct tm tml, *gmtime(), *localtime();
628:
629: extern time_t time();
630:
631: struct tm start_time, end_time, curr_time, last_time, forecast_time;
632: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
633: struct tm tm;
634:
635: char strcurr[80], strfor[80];
636:
637: char *endptr;
638: long lval;
639: double dval;
640:
641: #define NR_END 1
642: #define FREE_ARG char*
643: #define FTOL 1.0e-10
644:
645: #define NRANSI
646: #define ITMAX 200
647:
648: #define TOL 2.0e-4
649:
650: #define CGOLD 0.3819660
651: #define ZEPS 1.0e-10
652: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
653:
654: #define GOLD 1.618034
655: #define GLIMIT 100.0
656: #define TINY 1.0e-20
657:
658: static double maxarg1,maxarg2;
659: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
660: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
661:
662: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
663: #define rint(a) floor(a+0.5)
664:
665: static double sqrarg;
666: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
667: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
668: int agegomp= AGEGOMP;
669:
670: int imx;
671: int stepm=1;
672: /* Stepm, step in month: minimum step interpolation*/
673:
674: int estepm;
675: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
676:
677: int m,nb;
678: long *num;
679: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
680: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
681: double **pmmij, ***probs;
682: double *ageexmed,*agecens;
683: double dateintmean=0;
684:
685: double *weight;
686: int **s; /* Status */
687: double *agedc;
688: double **covar; /**< covar[j,i], value of jth covariate for individual i,
689: * covar=matrix(0,NCOVMAX,1,n);
690: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
691: double idx;
692: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
693: int *Ndum; /** Freq of modality (tricode */
694: int **codtab; /**< codtab=imatrix(1,100,1,10); */
695: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
696: double *lsurv, *lpop, *tpop;
697:
698: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
699: double ftolhess; /**< Tolerance for computing hessian */
700:
701: /**************** split *************************/
702: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
703: {
704: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
705: the name of the file (name), its extension only (ext) and its first part of the name (finame)
706: */
707: char *ss; /* pointer */
708: int l1, l2; /* length counters */
709:
710: l1 = strlen(path ); /* length of path */
711: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
712: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
713: if ( ss == NULL ) { /* no directory, so determine current directory */
714: strcpy( name, path ); /* we got the fullname name because no directory */
715: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
716: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
717: /* get current working directory */
718: /* extern char* getcwd ( char *buf , int len);*/
719: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
720: return( GLOCK_ERROR_GETCWD );
721: }
722: /* got dirc from getcwd*/
723: printf(" DIRC = %s \n",dirc);
724: } else { /* strip direcotry from path */
725: ss++; /* after this, the filename */
726: l2 = strlen( ss ); /* length of filename */
727: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
728: strcpy( name, ss ); /* save file name */
729: strncpy( dirc, path, l1 - l2 ); /* now the directory */
730: dirc[l1-l2] = 0; /* add zero */
731: printf(" DIRC2 = %s \n",dirc);
732: }
733: /* We add a separator at the end of dirc if not exists */
734: l1 = strlen( dirc ); /* length of directory */
735: if( dirc[l1-1] != DIRSEPARATOR ){
736: dirc[l1] = DIRSEPARATOR;
737: dirc[l1+1] = 0;
738: printf(" DIRC3 = %s \n",dirc);
739: }
740: ss = strrchr( name, '.' ); /* find last / */
741: if (ss >0){
742: ss++;
743: strcpy(ext,ss); /* save extension */
744: l1= strlen( name);
745: l2= strlen(ss)+1;
746: strncpy( finame, name, l1-l2);
747: finame[l1-l2]= 0;
748: }
749:
750: return( 0 ); /* we're done */
751: }
752:
753:
754: /******************************************/
755:
756: void replace_back_to_slash(char *s, char*t)
757: {
758: int i;
759: int lg=0;
760: i=0;
761: lg=strlen(t);
762: for(i=0; i<= lg; i++) {
763: (s[i] = t[i]);
764: if (t[i]== '\\') s[i]='/';
765: }
766: }
767:
768: char *trimbb(char *out, char *in)
769: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
770: char *s;
771: s=out;
772: while (*in != '\0'){
773: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
774: in++;
775: }
776: *out++ = *in++;
777: }
778: *out='\0';
779: return s;
780: }
781:
782: char *cutl(char *blocc, char *alocc, char *in, char occ)
783: {
784: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
785: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
786: gives blocc="abcdef2ghi" and alocc="j".
787: If occ is not found blocc is null and alocc is equal to in. Returns blocc
788: */
789: char *s, *t, *bl;
790: t=in;s=in;
791: while ((*in != occ) && (*in != '\0')){
792: *alocc++ = *in++;
793: }
794: if( *in == occ){
795: *(alocc)='\0';
796: s=++in;
797: }
798:
799: if (s == t) {/* occ not found */
800: *(alocc-(in-s))='\0';
801: in=s;
802: }
803: while ( *in != '\0'){
804: *blocc++ = *in++;
805: }
806:
807: *blocc='\0';
808: return t;
809: }
810: char *cutv(char *blocc, char *alocc, char *in, char occ)
811: {
812: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
813: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
814: gives blocc="abcdef2ghi" and alocc="j".
815: If occ is not found blocc is null and alocc is equal to in. Returns alocc
816: */
817: char *s, *t;
818: t=in;s=in;
819: while (*in != '\0'){
820: while( *in == occ){
821: *blocc++ = *in++;
822: s=in;
823: }
824: *blocc++ = *in++;
825: }
826: if (s == t) /* occ not found */
827: *(blocc-(in-s))='\0';
828: else
829: *(blocc-(in-s)-1)='\0';
830: in=s;
831: while ( *in != '\0'){
832: *alocc++ = *in++;
833: }
834:
835: *alocc='\0';
836: return s;
837: }
838:
839: int nbocc(char *s, char occ)
840: {
841: int i,j=0;
842: int lg=20;
843: i=0;
844: lg=strlen(s);
845: for(i=0; i<= lg; i++) {
846: if (s[i] == occ ) j++;
847: }
848: return j;
849: }
850:
851: /* void cutv(char *u,char *v, char*t, char occ) */
852: /* { */
853: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
854: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
855: /* gives u="abcdef2ghi" and v="j" *\/ */
856: /* int i,lg,j,p=0; */
857: /* i=0; */
858: /* lg=strlen(t); */
859: /* for(j=0; j<=lg-1; j++) { */
860: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
861: /* } */
862:
863: /* for(j=0; j<p; j++) { */
864: /* (u[j] = t[j]); */
865: /* } */
866: /* u[p]='\0'; */
867:
868: /* for(j=0; j<= lg; j++) { */
869: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
870: /* } */
871: /* } */
872:
873: /********************** nrerror ********************/
874:
875: void nrerror(char error_text[])
876: {
877: fprintf(stderr,"ERREUR ...\n");
878: fprintf(stderr,"%s\n",error_text);
879: exit(EXIT_FAILURE);
880: }
881: /*********************** vector *******************/
882: double *vector(int nl, int nh)
883: {
884: double *v;
885: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
886: if (!v) nrerror("allocation failure in vector");
887: return v-nl+NR_END;
888: }
889:
890: /************************ free vector ******************/
891: void free_vector(double*v, int nl, int nh)
892: {
893: free((FREE_ARG)(v+nl-NR_END));
894: }
895:
896: /************************ivector *******************************/
897: int *ivector(long nl,long nh)
898: {
899: int *v;
900: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
901: if (!v) nrerror("allocation failure in ivector");
902: return v-nl+NR_END;
903: }
904:
905: /******************free ivector **************************/
906: void free_ivector(int *v, long nl, long nh)
907: {
908: free((FREE_ARG)(v+nl-NR_END));
909: }
910:
911: /************************lvector *******************************/
912: long *lvector(long nl,long nh)
913: {
914: long *v;
915: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
916: if (!v) nrerror("allocation failure in ivector");
917: return v-nl+NR_END;
918: }
919:
920: /******************free lvector **************************/
921: void free_lvector(long *v, long nl, long nh)
922: {
923: free((FREE_ARG)(v+nl-NR_END));
924: }
925:
926: /******************* imatrix *******************************/
927: int **imatrix(long nrl, long nrh, long ncl, long nch)
928: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
929: {
930: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
931: int **m;
932:
933: /* allocate pointers to rows */
934: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
935: if (!m) nrerror("allocation failure 1 in matrix()");
936: m += NR_END;
937: m -= nrl;
938:
939:
940: /* allocate rows and set pointers to them */
941: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
942: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
943: m[nrl] += NR_END;
944: m[nrl] -= ncl;
945:
946: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
947:
948: /* return pointer to array of pointers to rows */
949: return m;
950: }
951:
952: /****************** free_imatrix *************************/
953: void free_imatrix(m,nrl,nrh,ncl,nch)
954: int **m;
955: long nch,ncl,nrh,nrl;
956: /* free an int matrix allocated by imatrix() */
957: {
958: free((FREE_ARG) (m[nrl]+ncl-NR_END));
959: free((FREE_ARG) (m+nrl-NR_END));
960: }
961:
962: /******************* matrix *******************************/
963: double **matrix(long nrl, long nrh, long ncl, long nch)
964: {
965: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
966: double **m;
967:
968: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
969: if (!m) nrerror("allocation failure 1 in matrix()");
970: m += NR_END;
971: m -= nrl;
972:
973: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
974: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
975: m[nrl] += NR_END;
976: m[nrl] -= ncl;
977:
978: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
979: return m;
980: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
981: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
982: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
983: */
984: }
985:
986: /*************************free matrix ************************/
987: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
988: {
989: free((FREE_ARG)(m[nrl]+ncl-NR_END));
990: free((FREE_ARG)(m+nrl-NR_END));
991: }
992:
993: /******************* ma3x *******************************/
994: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
995: {
996: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
997: double ***m;
998:
999: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1000: if (!m) nrerror("allocation failure 1 in matrix()");
1001: m += NR_END;
1002: m -= nrl;
1003:
1004: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1005: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1006: m[nrl] += NR_END;
1007: m[nrl] -= ncl;
1008:
1009: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1010:
1011: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1012: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1013: m[nrl][ncl] += NR_END;
1014: m[nrl][ncl] -= nll;
1015: for (j=ncl+1; j<=nch; j++)
1016: m[nrl][j]=m[nrl][j-1]+nlay;
1017:
1018: for (i=nrl+1; i<=nrh; i++) {
1019: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1020: for (j=ncl+1; j<=nch; j++)
1021: m[i][j]=m[i][j-1]+nlay;
1022: }
1023: return m;
1024: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1025: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1026: */
1027: }
1028:
1029: /*************************free ma3x ************************/
1030: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1031: {
1032: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1033: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1034: free((FREE_ARG)(m+nrl-NR_END));
1035: }
1036:
1037: /*************** function subdirf ***********/
1038: char *subdirf(char fileres[])
1039: {
1040: /* Caution optionfilefiname is hidden */
1041: strcpy(tmpout,optionfilefiname);
1042: strcat(tmpout,"/"); /* Add to the right */
1043: strcat(tmpout,fileres);
1044: return tmpout;
1045: }
1046:
1047: /*************** function subdirf2 ***********/
1048: char *subdirf2(char fileres[], char *preop)
1049: {
1050:
1051: /* Caution optionfilefiname is hidden */
1052: strcpy(tmpout,optionfilefiname);
1053: strcat(tmpout,"/");
1054: strcat(tmpout,preop);
1055: strcat(tmpout,fileres);
1056: return tmpout;
1057: }
1058:
1059: /*************** function subdirf3 ***********/
1060: char *subdirf3(char fileres[], char *preop, char *preop2)
1061: {
1062:
1063: /* Caution optionfilefiname is hidden */
1064: strcpy(tmpout,optionfilefiname);
1065: strcat(tmpout,"/");
1066: strcat(tmpout,preop);
1067: strcat(tmpout,preop2);
1068: strcat(tmpout,fileres);
1069: return tmpout;
1070: }
1071:
1072: /***************** f1dim *************************/
1073: extern int ncom;
1074: extern double *pcom,*xicom;
1075: extern double (*nrfunc)(double []);
1076:
1077: double f1dim(double x)
1078: {
1079: int j;
1080: double f;
1081: double *xt;
1082:
1083: xt=vector(1,ncom);
1084: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1085: f=(*nrfunc)(xt);
1086: free_vector(xt,1,ncom);
1087: return f;
1088: }
1089:
1090: /*****************brent *************************/
1091: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1092: {
1093: int iter;
1094: double a,b,d,etemp;
1095: double fu=0,fv,fw,fx;
1096: double ftemp;
1097: double p,q,r,tol1,tol2,u,v,w,x,xm;
1098: double e=0.0;
1099:
1100: a=(ax < cx ? ax : cx);
1101: b=(ax > cx ? ax : cx);
1102: x=w=v=bx;
1103: fw=fv=fx=(*f)(x);
1104: for (iter=1;iter<=ITMAX;iter++) {
1105: xm=0.5*(a+b);
1106: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1107: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1108: printf(".");fflush(stdout);
1109: fprintf(ficlog,".");fflush(ficlog);
1110: #ifdef DEBUG
1111: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1112: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
1113: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1114: #endif
1115: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1116: *xmin=x;
1117: return fx;
1118: }
1119: ftemp=fu;
1120: if (fabs(e) > tol1) {
1121: r=(x-w)*(fx-fv);
1122: q=(x-v)*(fx-fw);
1123: p=(x-v)*q-(x-w)*r;
1124: q=2.0*(q-r);
1125: if (q > 0.0) p = -p;
1126: q=fabs(q);
1127: etemp=e;
1128: e=d;
1129: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1130: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1131: else {
1132: d=p/q;
1133: u=x+d;
1134: if (u-a < tol2 || b-u < tol2)
1135: d=SIGN(tol1,xm-x);
1136: }
1137: } else {
1138: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1139: }
1140: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1141: fu=(*f)(u);
1142: if (fu <= fx) {
1143: if (u >= x) a=x; else b=x;
1144: SHFT(v,w,x,u)
1145: SHFT(fv,fw,fx,fu)
1146: } else {
1147: if (u < x) a=u; else b=u;
1148: if (fu <= fw || w == x) {
1149: v=w;
1150: w=u;
1151: fv=fw;
1152: fw=fu;
1153: } else if (fu <= fv || v == x || v == w) {
1154: v=u;
1155: fv=fu;
1156: }
1157: }
1158: }
1159: nrerror("Too many iterations in brent");
1160: *xmin=x;
1161: return fx;
1162: }
1163:
1164: /****************** mnbrak ***********************/
1165:
1166: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1167: double (*func)(double))
1168: {
1169: double ulim,u,r,q, dum;
1170: double fu;
1171:
1172: *fa=(*func)(*ax);
1173: *fb=(*func)(*bx);
1174: if (*fb > *fa) {
1175: SHFT(dum,*ax,*bx,dum)
1176: SHFT(dum,*fb,*fa,dum)
1177: }
1178: *cx=(*bx)+GOLD*(*bx-*ax);
1179: *fc=(*func)(*cx);
1180: while (*fb > *fc) {
1181: r=(*bx-*ax)*(*fb-*fc);
1182: q=(*bx-*cx)*(*fb-*fa);
1183: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1184: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1185: ulim=(*bx)+GLIMIT*(*cx-*bx);
1186: if ((*bx-u)*(u-*cx) > 0.0) {
1187: fu=(*func)(u);
1188: } else if ((*cx-u)*(u-ulim) > 0.0) {
1189: fu=(*func)(u);
1190: if (fu < *fc) {
1191: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1192: SHFT(*fb,*fc,fu,(*func)(u))
1193: }
1194: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1195: u=ulim;
1196: fu=(*func)(u);
1197: } else {
1198: u=(*cx)+GOLD*(*cx-*bx);
1199: fu=(*func)(u);
1200: }
1201: SHFT(*ax,*bx,*cx,u)
1202: SHFT(*fa,*fb,*fc,fu)
1203: }
1204: }
1205:
1206: /*************** linmin ************************/
1207:
1208: int ncom;
1209: double *pcom,*xicom;
1210: double (*nrfunc)(double []);
1211:
1212: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1213: {
1214: double brent(double ax, double bx, double cx,
1215: double (*f)(double), double tol, double *xmin);
1216: double f1dim(double x);
1217: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1218: double *fc, double (*func)(double));
1219: int j;
1220: double xx,xmin,bx,ax;
1221: double fx,fb,fa;
1222:
1223: ncom=n;
1224: pcom=vector(1,n);
1225: xicom=vector(1,n);
1226: nrfunc=func;
1227: for (j=1;j<=n;j++) {
1228: pcom[j]=p[j];
1229: xicom[j]=xi[j];
1230: }
1231: ax=0.0;
1232: xx=1.0;
1233: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1234: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1235: #ifdef DEBUG
1236: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1237: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1238: #endif
1239: for (j=1;j<=n;j++) {
1240: xi[j] *= xmin;
1241: p[j] += xi[j];
1242: }
1243: free_vector(xicom,1,n);
1244: free_vector(pcom,1,n);
1245: }
1246:
1247: char *asc_diff_time(long time_sec, char ascdiff[])
1248: {
1249: long sec_left, days, hours, minutes;
1250: days = (time_sec) / (60*60*24);
1251: sec_left = (time_sec) % (60*60*24);
1252: hours = (sec_left) / (60*60) ;
1253: sec_left = (sec_left) %(60*60);
1254: minutes = (sec_left) /60;
1255: sec_left = (sec_left) % (60);
1256: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1257: return ascdiff;
1258: }
1259:
1260: /*************** powell ************************/
1261: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1262: double (*func)(double []))
1263: {
1264: void linmin(double p[], double xi[], int n, double *fret,
1265: double (*func)(double []));
1266: int i,ibig,j;
1267: double del,t,*pt,*ptt,*xit;
1268: double fp,fptt;
1269: double *xits;
1270: int niterf, itmp;
1271:
1272: pt=vector(1,n);
1273: ptt=vector(1,n);
1274: xit=vector(1,n);
1275: xits=vector(1,n);
1276: *fret=(*func)(p);
1277: for (j=1;j<=n;j++) pt[j]=p[j];
1278: rcurr_time = time(NULL);
1279: for (*iter=1;;++(*iter)) {
1280: fp=(*fret);
1281: ibig=0;
1282: del=0.0;
1283: rlast_time=rcurr_time;
1284: /* (void) gettimeofday(&curr_time,&tzp); */
1285: rcurr_time = time(NULL);
1286: curr_time = *localtime(&rcurr_time);
1287: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1288: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1289: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1290: for (i=1;i<=n;i++) {
1291: printf(" %d %.12f",i, p[i]);
1292: fprintf(ficlog," %d %.12lf",i, p[i]);
1293: fprintf(ficrespow," %.12lf", p[i]);
1294: }
1295: printf("\n");
1296: fprintf(ficlog,"\n");
1297: fprintf(ficrespow,"\n");fflush(ficrespow);
1298: if(*iter <=3){
1299: tml = *localtime(&rcurr_time);
1300: strcpy(strcurr,asctime(&tml));
1301: /* asctime_r(&tm,strcurr); */
1302: rforecast_time=rcurr_time;
1303: itmp = strlen(strcurr);
1304: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1305: strcurr[itmp-1]='\0';
1306: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1307: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1308: for(niterf=10;niterf<=30;niterf+=10){
1309: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1310: forecast_time = *localtime(&rforecast_time);
1311: /* asctime_r(&tmf,strfor); */
1312: strcpy(strfor,asctime(&forecast_time));
1313: itmp = strlen(strfor);
1314: if(strfor[itmp-1]=='\n')
1315: strfor[itmp-1]='\0';
1316: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1317: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1318: }
1319: }
1320: for (i=1;i<=n;i++) {
1321: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1322: fptt=(*fret);
1323: #ifdef DEBUG
1324: printf("fret=%lf \n",*fret);
1325: fprintf(ficlog,"fret=%lf \n",*fret);
1326: #endif
1327: printf("%d",i);fflush(stdout);
1328: fprintf(ficlog,"%d",i);fflush(ficlog);
1329: linmin(p,xit,n,fret,func);
1330: if (fabs(fptt-(*fret)) > del) {
1331: del=fabs(fptt-(*fret));
1332: ibig=i;
1333: }
1334: #ifdef DEBUG
1335: printf("%d %.12e",i,(*fret));
1336: fprintf(ficlog,"%d %.12e",i,(*fret));
1337: for (j=1;j<=n;j++) {
1338: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1339: printf(" x(%d)=%.12e",j,xit[j]);
1340: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1341: }
1342: for(j=1;j<=n;j++) {
1343: printf(" p=%.12e",p[j]);
1344: fprintf(ficlog," p=%.12e",p[j]);
1345: }
1346: printf("\n");
1347: fprintf(ficlog,"\n");
1348: #endif
1349: }
1350: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1351: #ifdef DEBUG
1352: int k[2],l;
1353: k[0]=1;
1354: k[1]=-1;
1355: printf("Max: %.12e",(*func)(p));
1356: fprintf(ficlog,"Max: %.12e",(*func)(p));
1357: for (j=1;j<=n;j++) {
1358: printf(" %.12e",p[j]);
1359: fprintf(ficlog," %.12e",p[j]);
1360: }
1361: printf("\n");
1362: fprintf(ficlog,"\n");
1363: for(l=0;l<=1;l++) {
1364: for (j=1;j<=n;j++) {
1365: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1366: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1367: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1368: }
1369: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1370: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1371: }
1372: #endif
1373:
1374:
1375: free_vector(xit,1,n);
1376: free_vector(xits,1,n);
1377: free_vector(ptt,1,n);
1378: free_vector(pt,1,n);
1379: return;
1380: }
1381: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1382: for (j=1;j<=n;j++) {
1383: ptt[j]=2.0*p[j]-pt[j];
1384: xit[j]=p[j]-pt[j];
1385: pt[j]=p[j];
1386: }
1387: fptt=(*func)(ptt);
1388: if (fptt < fp) {
1389: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1390: if (t < 0.0) {
1391: linmin(p,xit,n,fret,func);
1392: for (j=1;j<=n;j++) {
1393: xi[j][ibig]=xi[j][n];
1394: xi[j][n]=xit[j];
1395: }
1396: #ifdef DEBUG
1397: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1398: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1399: for(j=1;j<=n;j++){
1400: printf(" %.12e",xit[j]);
1401: fprintf(ficlog," %.12e",xit[j]);
1402: }
1403: printf("\n");
1404: fprintf(ficlog,"\n");
1405: #endif
1406: }
1407: }
1408: }
1409: }
1410:
1411: /**** Prevalence limit (stable or period prevalence) ****************/
1412:
1413: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1414: {
1415: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1416: matrix by transitions matrix until convergence is reached */
1417:
1418: int i, ii,j,k;
1419: double min, max, maxmin, maxmax,sumnew=0.;
1420: /* double **matprod2(); */ /* test */
1421: double **out, cov[NCOVMAX+1], **pmij();
1422: double **newm;
1423: double agefin, delaymax=50 ; /* Max number of years to converge */
1424:
1425: for (ii=1;ii<=nlstate+ndeath;ii++)
1426: for (j=1;j<=nlstate+ndeath;j++){
1427: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1428: }
1429:
1430: cov[1]=1.;
1431:
1432: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1433: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1434: newm=savm;
1435: /* Covariates have to be included here again */
1436: cov[2]=agefin;
1437:
1438: for (k=1; k<=cptcovn;k++) {
1439: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1440: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1441: }
1442: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1443: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1444: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1445:
1446: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1447: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1448: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1449: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1450: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1451: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1452:
1453: savm=oldm;
1454: oldm=newm;
1455: maxmax=0.;
1456: for(j=1;j<=nlstate;j++){
1457: min=1.;
1458: max=0.;
1459: for(i=1; i<=nlstate; i++) {
1460: sumnew=0;
1461: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1462: prlim[i][j]= newm[i][j]/(1-sumnew);
1463: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1464: max=FMAX(max,prlim[i][j]);
1465: min=FMIN(min,prlim[i][j]);
1466: }
1467: maxmin=max-min;
1468: maxmax=FMAX(maxmax,maxmin);
1469: }
1470: if(maxmax < ftolpl){
1471: return prlim;
1472: }
1473: }
1474: }
1475:
1476: /*************** transition probabilities ***************/
1477:
1478: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1479: {
1480: /* According to parameters values stored in x and the covariate's values stored in cov,
1481: computes the probability to be observed in state j being in state i by appying the
1482: model to the ncovmodel covariates (including constant and age).
1483: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1484: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1485: ncth covariate in the global vector x is given by the formula:
1486: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1487: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1488: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1489: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1490: Outputs ps[i][j] the probability to be observed in j being in j according to
1491: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1492: */
1493: double s1, lnpijopii;
1494: /*double t34;*/
1495: int i,j,j1, nc, ii, jj;
1496:
1497: for(i=1; i<= nlstate; i++){
1498: for(j=1; j<i;j++){
1499: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1500: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1501: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1502: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1503: }
1504: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1505: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1506: }
1507: for(j=i+1; j<=nlstate+ndeath;j++){
1508: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1509: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1510: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1511: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1512: }
1513: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1514: }
1515: }
1516:
1517: for(i=1; i<= nlstate; i++){
1518: s1=0;
1519: for(j=1; j<i; j++){
1520: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1521: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1522: }
1523: for(j=i+1; j<=nlstate+ndeath; j++){
1524: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1525: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1526: }
1527: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1528: ps[i][i]=1./(s1+1.);
1529: /* Computing other pijs */
1530: for(j=1; j<i; j++)
1531: ps[i][j]= exp(ps[i][j])*ps[i][i];
1532: for(j=i+1; j<=nlstate+ndeath; j++)
1533: ps[i][j]= exp(ps[i][j])*ps[i][i];
1534: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1535: } /* end i */
1536:
1537: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1538: for(jj=1; jj<= nlstate+ndeath; jj++){
1539: ps[ii][jj]=0;
1540: ps[ii][ii]=1;
1541: }
1542: }
1543:
1544:
1545: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1546: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1547: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1548: /* } */
1549: /* printf("\n "); */
1550: /* } */
1551: /* printf("\n ");printf("%lf ",cov[2]);*/
1552: /*
1553: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1554: goto end;*/
1555: return ps;
1556: }
1557:
1558: /**************** Product of 2 matrices ******************/
1559:
1560: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1561: {
1562: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1563: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1564: /* in, b, out are matrice of pointers which should have been initialized
1565: before: only the contents of out is modified. The function returns
1566: a pointer to pointers identical to out */
1567: int i, j, k;
1568: for(i=nrl; i<= nrh; i++)
1569: for(k=ncolol; k<=ncoloh; k++){
1570: out[i][k]=0.;
1571: for(j=ncl; j<=nch; j++)
1572: out[i][k] +=in[i][j]*b[j][k];
1573: }
1574: return out;
1575: }
1576:
1577:
1578: /************* Higher Matrix Product ***************/
1579:
1580: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1581: {
1582: /* Computes the transition matrix starting at age 'age' over
1583: 'nhstepm*hstepm*stepm' months (i.e. until
1584: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1585: nhstepm*hstepm matrices.
1586: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1587: (typically every 2 years instead of every month which is too big
1588: for the memory).
1589: Model is determined by parameters x and covariates have to be
1590: included manually here.
1591:
1592: */
1593:
1594: int i, j, d, h, k;
1595: double **out, cov[NCOVMAX+1];
1596: double **newm;
1597:
1598: /* Hstepm could be zero and should return the unit matrix */
1599: for (i=1;i<=nlstate+ndeath;i++)
1600: for (j=1;j<=nlstate+ndeath;j++){
1601: oldm[i][j]=(i==j ? 1.0 : 0.0);
1602: po[i][j][0]=(i==j ? 1.0 : 0.0);
1603: }
1604: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1605: for(h=1; h <=nhstepm; h++){
1606: for(d=1; d <=hstepm; d++){
1607: newm=savm;
1608: /* Covariates have to be included here again */
1609: cov[1]=1.;
1610: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1611: for (k=1; k<=cptcovn;k++)
1612: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1613: for (k=1; k<=cptcovage;k++)
1614: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1615: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1616: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1617:
1618:
1619: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1620: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1621: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1622: pmij(pmmij,cov,ncovmodel,x,nlstate));
1623: savm=oldm;
1624: oldm=newm;
1625: }
1626: for(i=1; i<=nlstate+ndeath; i++)
1627: for(j=1;j<=nlstate+ndeath;j++) {
1628: po[i][j][h]=newm[i][j];
1629: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1630: }
1631: /*printf("h=%d ",h);*/
1632: } /* end h */
1633: /* printf("\n H=%d \n",h); */
1634: return po;
1635: }
1636:
1637:
1638: /*************** log-likelihood *************/
1639: double func( double *x)
1640: {
1641: int i, ii, j, k, mi, d, kk;
1642: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1643: double **out;
1644: double sw; /* Sum of weights */
1645: double lli; /* Individual log likelihood */
1646: int s1, s2;
1647: double bbh, survp;
1648: long ipmx;
1649: /*extern weight */
1650: /* We are differentiating ll according to initial status */
1651: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1652: /*for(i=1;i<imx;i++)
1653: printf(" %d\n",s[4][i]);
1654: */
1655: cov[1]=1.;
1656:
1657: for(k=1; k<=nlstate; k++) ll[k]=0.;
1658:
1659: if(mle==1){
1660: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1661: /* Computes the values of the ncovmodel covariates of the model
1662: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1663: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1664: to be observed in j being in i according to the model.
1665: */
1666: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1667: cov[2+k]=covar[Tvar[k]][i];
1668: }
1669: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1670: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1671: has been calculated etc */
1672: for(mi=1; mi<= wav[i]-1; mi++){
1673: for (ii=1;ii<=nlstate+ndeath;ii++)
1674: for (j=1;j<=nlstate+ndeath;j++){
1675: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1676: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1677: }
1678: for(d=0; d<dh[mi][i]; d++){
1679: newm=savm;
1680: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1681: for (kk=1; kk<=cptcovage;kk++) {
1682: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1683: }
1684: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1685: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1686: savm=oldm;
1687: oldm=newm;
1688: } /* end mult */
1689:
1690: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1691: /* But now since version 0.9 we anticipate for bias at large stepm.
1692: * If stepm is larger than one month (smallest stepm) and if the exact delay
1693: * (in months) between two waves is not a multiple of stepm, we rounded to
1694: * the nearest (and in case of equal distance, to the lowest) interval but now
1695: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1696: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1697: * probability in order to take into account the bias as a fraction of the way
1698: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1699: * -stepm/2 to stepm/2 .
1700: * For stepm=1 the results are the same as for previous versions of Imach.
1701: * For stepm > 1 the results are less biased than in previous versions.
1702: */
1703: s1=s[mw[mi][i]][i];
1704: s2=s[mw[mi+1][i]][i];
1705: bbh=(double)bh[mi][i]/(double)stepm;
1706: /* bias bh is positive if real duration
1707: * is higher than the multiple of stepm and negative otherwise.
1708: */
1709: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1710: if( s2 > nlstate){
1711: /* i.e. if s2 is a death state and if the date of death is known
1712: then the contribution to the likelihood is the probability to
1713: die between last step unit time and current step unit time,
1714: which is also equal to probability to die before dh
1715: minus probability to die before dh-stepm .
1716: In version up to 0.92 likelihood was computed
1717: as if date of death was unknown. Death was treated as any other
1718: health state: the date of the interview describes the actual state
1719: and not the date of a change in health state. The former idea was
1720: to consider that at each interview the state was recorded
1721: (healthy, disable or death) and IMaCh was corrected; but when we
1722: introduced the exact date of death then we should have modified
1723: the contribution of an exact death to the likelihood. This new
1724: contribution is smaller and very dependent of the step unit
1725: stepm. It is no more the probability to die between last interview
1726: and month of death but the probability to survive from last
1727: interview up to one month before death multiplied by the
1728: probability to die within a month. Thanks to Chris
1729: Jackson for correcting this bug. Former versions increased
1730: mortality artificially. The bad side is that we add another loop
1731: which slows down the processing. The difference can be up to 10%
1732: lower mortality.
1733: */
1734: lli=log(out[s1][s2] - savm[s1][s2]);
1735:
1736:
1737: } else if (s2==-2) {
1738: for (j=1,survp=0. ; j<=nlstate; j++)
1739: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1740: /*survp += out[s1][j]; */
1741: lli= log(survp);
1742: }
1743:
1744: else if (s2==-4) {
1745: for (j=3,survp=0. ; j<=nlstate; j++)
1746: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1747: lli= log(survp);
1748: }
1749:
1750: else if (s2==-5) {
1751: for (j=1,survp=0. ; j<=2; j++)
1752: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1753: lli= log(survp);
1754: }
1755:
1756: else{
1757: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1758: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
1759: }
1760: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1761: /*if(lli ==000.0)*/
1762: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1763: ipmx +=1;
1764: sw += weight[i];
1765: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1766: } /* end of wave */
1767: } /* end of individual */
1768: } else if(mle==2){
1769: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1770: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1771: for(mi=1; mi<= wav[i]-1; mi++){
1772: for (ii=1;ii<=nlstate+ndeath;ii++)
1773: for (j=1;j<=nlstate+ndeath;j++){
1774: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1775: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1776: }
1777: for(d=0; d<=dh[mi][i]; d++){
1778: newm=savm;
1779: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1780: for (kk=1; kk<=cptcovage;kk++) {
1781: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1782: }
1783: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1784: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1785: savm=oldm;
1786: oldm=newm;
1787: } /* end mult */
1788:
1789: s1=s[mw[mi][i]][i];
1790: s2=s[mw[mi+1][i]][i];
1791: bbh=(double)bh[mi][i]/(double)stepm;
1792: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1793: ipmx +=1;
1794: sw += weight[i];
1795: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1796: } /* end of wave */
1797: } /* end of individual */
1798: } else if(mle==3){ /* exponential inter-extrapolation */
1799: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1800: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1801: for(mi=1; mi<= wav[i]-1; mi++){
1802: for (ii=1;ii<=nlstate+ndeath;ii++)
1803: for (j=1;j<=nlstate+ndeath;j++){
1804: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1805: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1806: }
1807: for(d=0; d<dh[mi][i]; d++){
1808: newm=savm;
1809: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1810: for (kk=1; kk<=cptcovage;kk++) {
1811: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1812: }
1813: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1814: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1815: savm=oldm;
1816: oldm=newm;
1817: } /* end mult */
1818:
1819: s1=s[mw[mi][i]][i];
1820: s2=s[mw[mi+1][i]][i];
1821: bbh=(double)bh[mi][i]/(double)stepm;
1822: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1823: ipmx +=1;
1824: sw += weight[i];
1825: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1826: } /* end of wave */
1827: } /* end of individual */
1828: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1829: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1830: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1831: for(mi=1; mi<= wav[i]-1; mi++){
1832: for (ii=1;ii<=nlstate+ndeath;ii++)
1833: for (j=1;j<=nlstate+ndeath;j++){
1834: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1835: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1836: }
1837: for(d=0; d<dh[mi][i]; d++){
1838: newm=savm;
1839: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1840: for (kk=1; kk<=cptcovage;kk++) {
1841: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1842: }
1843:
1844: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1845: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1846: savm=oldm;
1847: oldm=newm;
1848: } /* end mult */
1849:
1850: s1=s[mw[mi][i]][i];
1851: s2=s[mw[mi+1][i]][i];
1852: if( s2 > nlstate){
1853: lli=log(out[s1][s2] - savm[s1][s2]);
1854: }else{
1855: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1856: }
1857: ipmx +=1;
1858: sw += weight[i];
1859: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1860: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1861: } /* end of wave */
1862: } /* end of individual */
1863: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1864: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1865: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1866: for(mi=1; mi<= wav[i]-1; mi++){
1867: for (ii=1;ii<=nlstate+ndeath;ii++)
1868: for (j=1;j<=nlstate+ndeath;j++){
1869: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1870: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1871: }
1872: for(d=0; d<dh[mi][i]; d++){
1873: newm=savm;
1874: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1875: for (kk=1; kk<=cptcovage;kk++) {
1876: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1877: }
1878:
1879: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1880: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1881: savm=oldm;
1882: oldm=newm;
1883: } /* end mult */
1884:
1885: s1=s[mw[mi][i]][i];
1886: s2=s[mw[mi+1][i]][i];
1887: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1888: ipmx +=1;
1889: sw += weight[i];
1890: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1891: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1892: } /* end of wave */
1893: } /* end of individual */
1894: } /* End of if */
1895: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1896: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1897: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1898: return -l;
1899: }
1900:
1901: /*************** log-likelihood *************/
1902: double funcone( double *x)
1903: {
1904: /* Same as likeli but slower because of a lot of printf and if */
1905: int i, ii, j, k, mi, d, kk;
1906: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1907: double **out;
1908: double lli; /* Individual log likelihood */
1909: double llt;
1910: int s1, s2;
1911: double bbh, survp;
1912: /*extern weight */
1913: /* We are differentiating ll according to initial status */
1914: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1915: /*for(i=1;i<imx;i++)
1916: printf(" %d\n",s[4][i]);
1917: */
1918: cov[1]=1.;
1919:
1920: for(k=1; k<=nlstate; k++) ll[k]=0.;
1921:
1922: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1923: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1924: for(mi=1; mi<= wav[i]-1; mi++){
1925: for (ii=1;ii<=nlstate+ndeath;ii++)
1926: for (j=1;j<=nlstate+ndeath;j++){
1927: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1928: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1929: }
1930: for(d=0; d<dh[mi][i]; d++){
1931: newm=savm;
1932: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1933: for (kk=1; kk<=cptcovage;kk++) {
1934: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1935: }
1936: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1937: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1938: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1939: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1940: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1941: savm=oldm;
1942: oldm=newm;
1943: } /* end mult */
1944:
1945: s1=s[mw[mi][i]][i];
1946: s2=s[mw[mi+1][i]][i];
1947: bbh=(double)bh[mi][i]/(double)stepm;
1948: /* bias is positive if real duration
1949: * is higher than the multiple of stepm and negative otherwise.
1950: */
1951: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1952: lli=log(out[s1][s2] - savm[s1][s2]);
1953: } else if (s2==-2) {
1954: for (j=1,survp=0. ; j<=nlstate; j++)
1955: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1956: lli= log(survp);
1957: }else if (mle==1){
1958: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1959: } else if(mle==2){
1960: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1961: } else if(mle==3){ /* exponential inter-extrapolation */
1962: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1963: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1964: lli=log(out[s1][s2]); /* Original formula */
1965: } else{ /* mle=0 back to 1 */
1966: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1967: /*lli=log(out[s1][s2]); */ /* Original formula */
1968: } /* End of if */
1969: ipmx +=1;
1970: sw += weight[i];
1971: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1972: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1973: if(globpr){
1974: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1975: %11.6f %11.6f %11.6f ", \
1976: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1977: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1978: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1979: llt +=ll[k]*gipmx/gsw;
1980: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1981: }
1982: fprintf(ficresilk," %10.6f\n", -llt);
1983: }
1984: } /* end of wave */
1985: } /* end of individual */
1986: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1987: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1988: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1989: if(globpr==0){ /* First time we count the contributions and weights */
1990: gipmx=ipmx;
1991: gsw=sw;
1992: }
1993: return -l;
1994: }
1995:
1996:
1997: /*************** function likelione ***********/
1998: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1999: {
2000: /* This routine should help understanding what is done with
2001: the selection of individuals/waves and
2002: to check the exact contribution to the likelihood.
2003: Plotting could be done.
2004: */
2005: int k;
2006:
2007: if(*globpri !=0){ /* Just counts and sums, no printings */
2008: strcpy(fileresilk,"ilk");
2009: strcat(fileresilk,fileres);
2010: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2011: printf("Problem with resultfile: %s\n", fileresilk);
2012: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2013: }
2014: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
2015: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2016: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2017: for(k=1; k<=nlstate; k++)
2018: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2019: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2020: }
2021:
2022: *fretone=(*funcone)(p);
2023: if(*globpri !=0){
2024: fclose(ficresilk);
2025: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2026: fflush(fichtm);
2027: }
2028: return;
2029: }
2030:
2031:
2032: /*********** Maximum Likelihood Estimation ***************/
2033:
2034: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2035: {
2036: int i,j, iter;
2037: double **xi;
2038: double fret;
2039: double fretone; /* Only one call to likelihood */
2040: /* char filerespow[FILENAMELENGTH];*/
2041: xi=matrix(1,npar,1,npar);
2042: for (i=1;i<=npar;i++)
2043: for (j=1;j<=npar;j++)
2044: xi[i][j]=(i==j ? 1.0 : 0.0);
2045: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2046: strcpy(filerespow,"pow");
2047: strcat(filerespow,fileres);
2048: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2049: printf("Problem with resultfile: %s\n", filerespow);
2050: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2051: }
2052: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2053: for (i=1;i<=nlstate;i++)
2054: for(j=1;j<=nlstate+ndeath;j++)
2055: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2056: fprintf(ficrespow,"\n");
2057:
2058: powell(p,xi,npar,ftol,&iter,&fret,func);
2059:
2060: free_matrix(xi,1,npar,1,npar);
2061: fclose(ficrespow);
2062: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2063: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2064: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2065:
2066: }
2067:
2068: /**** Computes Hessian and covariance matrix ***/
2069: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2070: {
2071: double **a,**y,*x,pd;
2072: double **hess;
2073: int i, j,jk;
2074: int *indx;
2075:
2076: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2077: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2078: void lubksb(double **a, int npar, int *indx, double b[]) ;
2079: void ludcmp(double **a, int npar, int *indx, double *d) ;
2080: double gompertz(double p[]);
2081: hess=matrix(1,npar,1,npar);
2082:
2083: printf("\nCalculation of the hessian matrix. Wait...\n");
2084: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2085: for (i=1;i<=npar;i++){
2086: printf("%d",i);fflush(stdout);
2087: fprintf(ficlog,"%d",i);fflush(ficlog);
2088:
2089: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2090:
2091: /* printf(" %f ",p[i]);
2092: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2093: }
2094:
2095: for (i=1;i<=npar;i++) {
2096: for (j=1;j<=npar;j++) {
2097: if (j>i) {
2098: printf(".%d%d",i,j);fflush(stdout);
2099: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2100: hess[i][j]=hessij(p,delti,i,j,func,npar);
2101:
2102: hess[j][i]=hess[i][j];
2103: /*printf(" %lf ",hess[i][j]);*/
2104: }
2105: }
2106: }
2107: printf("\n");
2108: fprintf(ficlog,"\n");
2109:
2110: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2111: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2112:
2113: a=matrix(1,npar,1,npar);
2114: y=matrix(1,npar,1,npar);
2115: x=vector(1,npar);
2116: indx=ivector(1,npar);
2117: for (i=1;i<=npar;i++)
2118: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2119: ludcmp(a,npar,indx,&pd);
2120:
2121: for (j=1;j<=npar;j++) {
2122: for (i=1;i<=npar;i++) x[i]=0;
2123: x[j]=1;
2124: lubksb(a,npar,indx,x);
2125: for (i=1;i<=npar;i++){
2126: matcov[i][j]=x[i];
2127: }
2128: }
2129:
2130: printf("\n#Hessian matrix#\n");
2131: fprintf(ficlog,"\n#Hessian matrix#\n");
2132: for (i=1;i<=npar;i++) {
2133: for (j=1;j<=npar;j++) {
2134: printf("%.3e ",hess[i][j]);
2135: fprintf(ficlog,"%.3e ",hess[i][j]);
2136: }
2137: printf("\n");
2138: fprintf(ficlog,"\n");
2139: }
2140:
2141: /* Recompute Inverse */
2142: for (i=1;i<=npar;i++)
2143: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2144: ludcmp(a,npar,indx,&pd);
2145:
2146: /* printf("\n#Hessian matrix recomputed#\n");
2147:
2148: for (j=1;j<=npar;j++) {
2149: for (i=1;i<=npar;i++) x[i]=0;
2150: x[j]=1;
2151: lubksb(a,npar,indx,x);
2152: for (i=1;i<=npar;i++){
2153: y[i][j]=x[i];
2154: printf("%.3e ",y[i][j]);
2155: fprintf(ficlog,"%.3e ",y[i][j]);
2156: }
2157: printf("\n");
2158: fprintf(ficlog,"\n");
2159: }
2160: */
2161:
2162: free_matrix(a,1,npar,1,npar);
2163: free_matrix(y,1,npar,1,npar);
2164: free_vector(x,1,npar);
2165: free_ivector(indx,1,npar);
2166: free_matrix(hess,1,npar,1,npar);
2167:
2168:
2169: }
2170:
2171: /*************** hessian matrix ****************/
2172: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2173: {
2174: int i;
2175: int l=1, lmax=20;
2176: double k1,k2;
2177: double p2[MAXPARM+1]; /* identical to x */
2178: double res;
2179: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2180: double fx;
2181: int k=0,kmax=10;
2182: double l1;
2183:
2184: fx=func(x);
2185: for (i=1;i<=npar;i++) p2[i]=x[i];
2186: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2187: l1=pow(10,l);
2188: delts=delt;
2189: for(k=1 ; k <kmax; k=k+1){
2190: delt = delta*(l1*k);
2191: p2[theta]=x[theta] +delt;
2192: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2193: p2[theta]=x[theta]-delt;
2194: k2=func(p2)-fx;
2195: /*res= (k1-2.0*fx+k2)/delt/delt; */
2196: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2197:
2198: #ifdef DEBUGHESS
2199: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
2200: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
2201: #endif
2202: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2203: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2204: k=kmax;
2205: }
2206: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2207: k=kmax; l=lmax*10.;
2208: }
2209: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2210: delts=delt;
2211: }
2212: }
2213: }
2214: delti[theta]=delts;
2215: return res;
2216:
2217: }
2218:
2219: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2220: {
2221: int i;
2222: int l=1, l1, lmax=20;
2223: double k1,k2,k3,k4,res,fx;
2224: double p2[MAXPARM+1];
2225: int k;
2226:
2227: fx=func(x);
2228: for (k=1; k<=2; k++) {
2229: for (i=1;i<=npar;i++) p2[i]=x[i];
2230: p2[thetai]=x[thetai]+delti[thetai]/k;
2231: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2232: k1=func(p2)-fx;
2233:
2234: p2[thetai]=x[thetai]+delti[thetai]/k;
2235: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2236: k2=func(p2)-fx;
2237:
2238: p2[thetai]=x[thetai]-delti[thetai]/k;
2239: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2240: k3=func(p2)-fx;
2241:
2242: p2[thetai]=x[thetai]-delti[thetai]/k;
2243: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2244: k4=func(p2)-fx;
2245: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2246: #ifdef DEBUG
2247: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
2248: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
2249: #endif
2250: }
2251: return res;
2252: }
2253:
2254: /************** Inverse of matrix **************/
2255: void ludcmp(double **a, int n, int *indx, double *d)
2256: {
2257: int i,imax,j,k;
2258: double big,dum,sum,temp;
2259: double *vv;
2260:
2261: vv=vector(1,n);
2262: *d=1.0;
2263: for (i=1;i<=n;i++) {
2264: big=0.0;
2265: for (j=1;j<=n;j++)
2266: if ((temp=fabs(a[i][j])) > big) big=temp;
2267: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2268: vv[i]=1.0/big;
2269: }
2270: for (j=1;j<=n;j++) {
2271: for (i=1;i<j;i++) {
2272: sum=a[i][j];
2273: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2274: a[i][j]=sum;
2275: }
2276: big=0.0;
2277: for (i=j;i<=n;i++) {
2278: sum=a[i][j];
2279: for (k=1;k<j;k++)
2280: sum -= a[i][k]*a[k][j];
2281: a[i][j]=sum;
2282: if ( (dum=vv[i]*fabs(sum)) >= big) {
2283: big=dum;
2284: imax=i;
2285: }
2286: }
2287: if (j != imax) {
2288: for (k=1;k<=n;k++) {
2289: dum=a[imax][k];
2290: a[imax][k]=a[j][k];
2291: a[j][k]=dum;
2292: }
2293: *d = -(*d);
2294: vv[imax]=vv[j];
2295: }
2296: indx[j]=imax;
2297: if (a[j][j] == 0.0) a[j][j]=TINY;
2298: if (j != n) {
2299: dum=1.0/(a[j][j]);
2300: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2301: }
2302: }
2303: free_vector(vv,1,n); /* Doesn't work */
2304: ;
2305: }
2306:
2307: void lubksb(double **a, int n, int *indx, double b[])
2308: {
2309: int i,ii=0,ip,j;
2310: double sum;
2311:
2312: for (i=1;i<=n;i++) {
2313: ip=indx[i];
2314: sum=b[ip];
2315: b[ip]=b[i];
2316: if (ii)
2317: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2318: else if (sum) ii=i;
2319: b[i]=sum;
2320: }
2321: for (i=n;i>=1;i--) {
2322: sum=b[i];
2323: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2324: b[i]=sum/a[i][i];
2325: }
2326: }
2327:
2328: void pstamp(FILE *fichier)
2329: {
2330: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2331: }
2332:
2333: /************ Frequencies ********************/
2334: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
2335: { /* Some frequencies */
2336:
2337: int i, m, jk, k1,i1, j1, bool, z1,j;
2338: int first;
2339: double ***freq; /* Frequencies */
2340: double *pp, **prop;
2341: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2342: char fileresp[FILENAMELENGTH];
2343:
2344: pp=vector(1,nlstate);
2345: prop=matrix(1,nlstate,iagemin,iagemax+3);
2346: strcpy(fileresp,"p");
2347: strcat(fileresp,fileres);
2348: if((ficresp=fopen(fileresp,"w"))==NULL) {
2349: printf("Problem with prevalence resultfile: %s\n", fileresp);
2350: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2351: exit(0);
2352: }
2353: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2354: j1=0;
2355:
2356: j=cptcoveff;
2357: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2358:
2359: first=1;
2360:
2361: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2362: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2363: /* j1++;
2364: */
2365: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2366: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2367: scanf("%d", i);*/
2368: for (i=-5; i<=nlstate+ndeath; i++)
2369: for (jk=-5; jk<=nlstate+ndeath; jk++)
2370: for(m=iagemin; m <= iagemax+3; m++)
2371: freq[i][jk][m]=0;
2372:
2373: for (i=1; i<=nlstate; i++)
2374: for(m=iagemin; m <= iagemax+3; m++)
2375: prop[i][m]=0;
2376:
2377: dateintsum=0;
2378: k2cpt=0;
2379: for (i=1; i<=imx; i++) {
2380: bool=1;
2381: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2382: for (z1=1; z1<=cptcoveff; z1++)
2383: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2384: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2385: bool=0;
2386: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2387: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2388: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2389: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2390: }
2391: }
2392:
2393: if (bool==1){
2394: for(m=firstpass; m<=lastpass; m++){
2395: k2=anint[m][i]+(mint[m][i]/12.);
2396: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2397: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2398: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2399: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2400: if (m<lastpass) {
2401: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2402: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2403: }
2404:
2405: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2406: dateintsum=dateintsum+k2;
2407: k2cpt++;
2408: }
2409: /*}*/
2410: }
2411: }
2412: } /* end i */
2413:
2414: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2415: pstamp(ficresp);
2416: if (cptcovn>0) {
2417: fprintf(ficresp, "\n#********** Variable ");
2418: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2419: fprintf(ficresp, "**********\n#");
2420: fprintf(ficlog, "\n#********** Variable ");
2421: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2422: fprintf(ficlog, "**********\n#");
2423: }
2424: for(i=1; i<=nlstate;i++)
2425: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2426: fprintf(ficresp, "\n");
2427:
2428: for(i=iagemin; i <= iagemax+3; i++){
2429: if(i==iagemax+3){
2430: fprintf(ficlog,"Total");
2431: }else{
2432: if(first==1){
2433: first=0;
2434: printf("See log file for details...\n");
2435: }
2436: fprintf(ficlog,"Age %d", i);
2437: }
2438: for(jk=1; jk <=nlstate ; jk++){
2439: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2440: pp[jk] += freq[jk][m][i];
2441: }
2442: for(jk=1; jk <=nlstate ; jk++){
2443: for(m=-1, pos=0; m <=0 ; m++)
2444: pos += freq[jk][m][i];
2445: if(pp[jk]>=1.e-10){
2446: if(first==1){
2447: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2448: }
2449: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2450: }else{
2451: if(first==1)
2452: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2453: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2454: }
2455: }
2456:
2457: for(jk=1; jk <=nlstate ; jk++){
2458: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2459: pp[jk] += freq[jk][m][i];
2460: }
2461: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2462: pos += pp[jk];
2463: posprop += prop[jk][i];
2464: }
2465: for(jk=1; jk <=nlstate ; jk++){
2466: if(pos>=1.e-5){
2467: if(first==1)
2468: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2469: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2470: }else{
2471: if(first==1)
2472: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2473: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2474: }
2475: if( i <= iagemax){
2476: if(pos>=1.e-5){
2477: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2478: /*probs[i][jk][j1]= pp[jk]/pos;*/
2479: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2480: }
2481: else
2482: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2483: }
2484: }
2485:
2486: for(jk=-1; jk <=nlstate+ndeath; jk++)
2487: for(m=-1; m <=nlstate+ndeath; m++)
2488: if(freq[jk][m][i] !=0 ) {
2489: if(first==1)
2490: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2491: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2492: }
2493: if(i <= iagemax)
2494: fprintf(ficresp,"\n");
2495: if(first==1)
2496: printf("Others in log...\n");
2497: fprintf(ficlog,"\n");
2498: }
2499: /*}*/
2500: }
2501: dateintmean=dateintsum/k2cpt;
2502:
2503: fclose(ficresp);
2504: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2505: free_vector(pp,1,nlstate);
2506: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2507: /* End of Freq */
2508: }
2509:
2510: /************ Prevalence ********************/
2511: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
2512: {
2513: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2514: in each health status at the date of interview (if between dateprev1 and dateprev2).
2515: We still use firstpass and lastpass as another selection.
2516: */
2517:
2518: int i, m, jk, k1, i1, j1, bool, z1,j;
2519: double ***freq; /* Frequencies */
2520: double *pp, **prop;
2521: double pos,posprop;
2522: double y2; /* in fractional years */
2523: int iagemin, iagemax;
2524: int first; /** to stop verbosity which is redirected to log file */
2525:
2526: iagemin= (int) agemin;
2527: iagemax= (int) agemax;
2528: /*pp=vector(1,nlstate);*/
2529: prop=matrix(1,nlstate,iagemin,iagemax+3);
2530: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2531: j1=0;
2532:
2533: /*j=cptcoveff;*/
2534: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2535:
2536: first=1;
2537: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2538: /*for(i1=1; i1<=ncodemax[k1];i1++){
2539: j1++;*/
2540:
2541: for (i=1; i<=nlstate; i++)
2542: for(m=iagemin; m <= iagemax+3; m++)
2543: prop[i][m]=0.0;
2544:
2545: for (i=1; i<=imx; i++) { /* Each individual */
2546: bool=1;
2547: if (cptcovn>0) {
2548: for (z1=1; z1<=cptcoveff; z1++)
2549: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2550: bool=0;
2551: }
2552: if (bool==1) {
2553: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2554: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2555: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2556: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2557: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2558: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
2559: if (s[m][i]>0 && s[m][i]<=nlstate) {
2560: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
2561: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2562: prop[s[m][i]][iagemax+3] += weight[i];
2563: }
2564: }
2565: } /* end selection of waves */
2566: }
2567: }
2568: for(i=iagemin; i <= iagemax+3; i++){
2569: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2570: posprop += prop[jk][i];
2571: }
2572:
2573: for(jk=1; jk <=nlstate ; jk++){
2574: if( i <= iagemax){
2575: if(posprop>=1.e-5){
2576: probs[i][jk][j1]= prop[jk][i]/posprop;
2577: } else{
2578: if(first==1){
2579: first=0;
2580: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
2581: }
2582: }
2583: }
2584: }/* end jk */
2585: }/* end i */
2586: /*} *//* end i1 */
2587: } /* end j1 */
2588:
2589: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2590: /*free_vector(pp,1,nlstate);*/
2591: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2592: } /* End of prevalence */
2593:
2594: /************* Waves Concatenation ***************/
2595:
2596: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
2597: {
2598: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2599: Death is a valid wave (if date is known).
2600: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2601: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2602: and mw[mi+1][i]. dh depends on stepm.
2603: */
2604:
2605: int i, mi, m;
2606: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2607: double sum=0., jmean=0.;*/
2608: int first;
2609: int j, k=0,jk, ju, jl;
2610: double sum=0.;
2611: first=0;
2612: jmin=1e+5;
2613: jmax=-1;
2614: jmean=0.;
2615: for(i=1; i<=imx; i++){
2616: mi=0;
2617: m=firstpass;
2618: while(s[m][i] <= nlstate){
2619: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2620: mw[++mi][i]=m;
2621: if(m >=lastpass)
2622: break;
2623: else
2624: m++;
2625: }/* end while */
2626: if (s[m][i] > nlstate){
2627: mi++; /* Death is another wave */
2628: /* if(mi==0) never been interviewed correctly before death */
2629: /* Only death is a correct wave */
2630: mw[mi][i]=m;
2631: }
2632:
2633: wav[i]=mi;
2634: if(mi==0){
2635: nbwarn++;
2636: if(first==0){
2637: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2638: first=1;
2639: }
2640: if(first==1){
2641: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2642: }
2643: } /* end mi==0 */
2644: } /* End individuals */
2645:
2646: for(i=1; i<=imx; i++){
2647: for(mi=1; mi<wav[i];mi++){
2648: if (stepm <=0)
2649: dh[mi][i]=1;
2650: else{
2651: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2652: if (agedc[i] < 2*AGESUP) {
2653: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2654: if(j==0) j=1; /* Survives at least one month after exam */
2655: else if(j<0){
2656: nberr++;
2657: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2658: j=1; /* Temporary Dangerous patch */
2659: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
2660: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2661: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
2662: }
2663: k=k+1;
2664: if (j >= jmax){
2665: jmax=j;
2666: ijmax=i;
2667: }
2668: if (j <= jmin){
2669: jmin=j;
2670: ijmin=i;
2671: }
2672: sum=sum+j;
2673: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2674: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2675: }
2676: }
2677: else{
2678: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2679: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
2680:
2681: k=k+1;
2682: if (j >= jmax) {
2683: jmax=j;
2684: ijmax=i;
2685: }
2686: else if (j <= jmin){
2687: jmin=j;
2688: ijmin=i;
2689: }
2690: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2691: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
2692: if(j<0){
2693: nberr++;
2694: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2695: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2696: }
2697: sum=sum+j;
2698: }
2699: jk= j/stepm;
2700: jl= j -jk*stepm;
2701: ju= j -(jk+1)*stepm;
2702: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2703: if(jl==0){
2704: dh[mi][i]=jk;
2705: bh[mi][i]=0;
2706: }else{ /* We want a negative bias in order to only have interpolation ie
2707: * to avoid the price of an extra matrix product in likelihood */
2708: dh[mi][i]=jk+1;
2709: bh[mi][i]=ju;
2710: }
2711: }else{
2712: if(jl <= -ju){
2713: dh[mi][i]=jk;
2714: bh[mi][i]=jl; /* bias is positive if real duration
2715: * is higher than the multiple of stepm and negative otherwise.
2716: */
2717: }
2718: else{
2719: dh[mi][i]=jk+1;
2720: bh[mi][i]=ju;
2721: }
2722: if(dh[mi][i]==0){
2723: dh[mi][i]=1; /* At least one step */
2724: bh[mi][i]=ju; /* At least one step */
2725: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
2726: }
2727: } /* end if mle */
2728: }
2729: } /* end wave */
2730: }
2731: jmean=sum/k;
2732: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
2733: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2734: }
2735:
2736: /*********** Tricode ****************************/
2737: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2738: {
2739: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2740: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2741: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2742: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2743: /* nbcode[Tvar[j]][1]=
2744: */
2745:
2746: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2747: int modmaxcovj=0; /* Modality max of covariates j */
2748: int cptcode=0; /* Modality max of covariates j */
2749: int modmincovj=0; /* Modality min of covariates j */
2750:
2751:
2752: cptcoveff=0;
2753:
2754: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2755: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2756:
2757: /* Loop on covariates without age and products */
2758: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2759: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2760: modality of this covariate Vj*/
2761: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2762: * If product of Vn*Vm, still boolean *:
2763: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2764: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2765: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2766: modality of the nth covariate of individual i. */
2767: if (ij > modmaxcovj)
2768: modmaxcovj=ij;
2769: else if (ij < modmincovj)
2770: modmincovj=ij;
2771: if ((ij < -1) && (ij > NCOVMAX)){
2772: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2773: exit(1);
2774: }else
2775: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2776: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2777: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2778: /* getting the maximum value of the modality of the covariate
2779: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2780: female is 1, then modmaxcovj=1.*/
2781: }
2782: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2783: cptcode=modmaxcovj;
2784: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2785: /*for (i=0; i<=cptcode; i++) {*/
2786: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2787: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2788: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2789: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2790: }
2791: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2792: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2793: } /* Ndum[-1] number of undefined modalities */
2794:
2795: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2796: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2797: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2798: modmincovj=3; modmaxcovj = 7;
2799: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2800: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2801: variables V1_1 and V1_2.
2802: nbcode[Tvar[j]][ij]=k;
2803: nbcode[Tvar[j]][1]=0;
2804: nbcode[Tvar[j]][2]=1;
2805: nbcode[Tvar[j]][3]=2;
2806: */
2807: ij=1; /* ij is similar to i but can jumps over null modalities */
2808: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2809: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2810: /*recode from 0 */
2811: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2812: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2813: k is a modality. If we have model=V1+V1*sex
2814: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2815: ij++;
2816: }
2817: if (ij > ncodemax[j]) break;
2818: } /* end of loop on */
2819: } /* end of loop on modality */
2820: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2821:
2822: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2823:
2824: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2825: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2826: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2827: Ndum[ij]++;
2828: }
2829:
2830: ij=1;
2831: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2832: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2833: if((Ndum[i]!=0) && (i<=ncovcol)){
2834: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2835: Tvaraff[ij]=i; /*For printing (unclear) */
2836: ij++;
2837: }else
2838: Tvaraff[ij]=0;
2839: }
2840: ij--;
2841: cptcoveff=ij; /*Number of total covariates*/
2842:
2843: }
2844:
2845:
2846: /*********** Health Expectancies ****************/
2847:
2848: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2849:
2850: {
2851: /* Health expectancies, no variances */
2852: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2853: int nhstepma, nstepma; /* Decreasing with age */
2854: double age, agelim, hf;
2855: double ***p3mat;
2856: double eip;
2857:
2858: pstamp(ficreseij);
2859: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2860: fprintf(ficreseij,"# Age");
2861: for(i=1; i<=nlstate;i++){
2862: for(j=1; j<=nlstate;j++){
2863: fprintf(ficreseij," e%1d%1d ",i,j);
2864: }
2865: fprintf(ficreseij," e%1d. ",i);
2866: }
2867: fprintf(ficreseij,"\n");
2868:
2869:
2870: if(estepm < stepm){
2871: printf ("Problem %d lower than %d\n",estepm, stepm);
2872: }
2873: else hstepm=estepm;
2874: /* We compute the life expectancy from trapezoids spaced every estepm months
2875: * This is mainly to measure the difference between two models: for example
2876: * if stepm=24 months pijx are given only every 2 years and by summing them
2877: * we are calculating an estimate of the Life Expectancy assuming a linear
2878: * progression in between and thus overestimating or underestimating according
2879: * to the curvature of the survival function. If, for the same date, we
2880: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2881: * to compare the new estimate of Life expectancy with the same linear
2882: * hypothesis. A more precise result, taking into account a more precise
2883: * curvature will be obtained if estepm is as small as stepm. */
2884:
2885: /* For example we decided to compute the life expectancy with the smallest unit */
2886: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2887: nhstepm is the number of hstepm from age to agelim
2888: nstepm is the number of stepm from age to agelin.
2889: Look at hpijx to understand the reason of that which relies in memory size
2890: and note for a fixed period like estepm months */
2891: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2892: survival function given by stepm (the optimization length). Unfortunately it
2893: means that if the survival funtion is printed only each two years of age and if
2894: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2895: results. So we changed our mind and took the option of the best precision.
2896: */
2897: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2898:
2899: agelim=AGESUP;
2900: /* If stepm=6 months */
2901: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2902: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2903:
2904: /* nhstepm age range expressed in number of stepm */
2905: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2906: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2907: /* if (stepm >= YEARM) hstepm=1;*/
2908: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2909: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2910:
2911: for (age=bage; age<=fage; age ++){
2912: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2913: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2914: /* if (stepm >= YEARM) hstepm=1;*/
2915: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2916:
2917: /* If stepm=6 months */
2918: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2919: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2920:
2921: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2922:
2923: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2924:
2925: printf("%d|",(int)age);fflush(stdout);
2926: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2927:
2928: /* Computing expectancies */
2929: for(i=1; i<=nlstate;i++)
2930: for(j=1; j<=nlstate;j++)
2931: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2932: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2933:
2934: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
2935:
2936: }
2937:
2938: fprintf(ficreseij,"%3.0f",age );
2939: for(i=1; i<=nlstate;i++){
2940: eip=0;
2941: for(j=1; j<=nlstate;j++){
2942: eip +=eij[i][j][(int)age];
2943: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2944: }
2945: fprintf(ficreseij,"%9.4f", eip );
2946: }
2947: fprintf(ficreseij,"\n");
2948:
2949: }
2950: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2951: printf("\n");
2952: fprintf(ficlog,"\n");
2953:
2954: }
2955:
2956: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
2957:
2958: {
2959: /* Covariances of health expectancies eij and of total life expectancies according
2960: to initial status i, ei. .
2961: */
2962: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2963: int nhstepma, nstepma; /* Decreasing with age */
2964: double age, agelim, hf;
2965: double ***p3matp, ***p3matm, ***varhe;
2966: double **dnewm,**doldm;
2967: double *xp, *xm;
2968: double **gp, **gm;
2969: double ***gradg, ***trgradg;
2970: int theta;
2971:
2972: double eip, vip;
2973:
2974: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2975: xp=vector(1,npar);
2976: xm=vector(1,npar);
2977: dnewm=matrix(1,nlstate*nlstate,1,npar);
2978: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2979:
2980: pstamp(ficresstdeij);
2981: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2982: fprintf(ficresstdeij,"# Age");
2983: for(i=1; i<=nlstate;i++){
2984: for(j=1; j<=nlstate;j++)
2985: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2986: fprintf(ficresstdeij," e%1d. ",i);
2987: }
2988: fprintf(ficresstdeij,"\n");
2989:
2990: pstamp(ficrescveij);
2991: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2992: fprintf(ficrescveij,"# Age");
2993: for(i=1; i<=nlstate;i++)
2994: for(j=1; j<=nlstate;j++){
2995: cptj= (j-1)*nlstate+i;
2996: for(i2=1; i2<=nlstate;i2++)
2997: for(j2=1; j2<=nlstate;j2++){
2998: cptj2= (j2-1)*nlstate+i2;
2999: if(cptj2 <= cptj)
3000: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3001: }
3002: }
3003: fprintf(ficrescveij,"\n");
3004:
3005: if(estepm < stepm){
3006: printf ("Problem %d lower than %d\n",estepm, stepm);
3007: }
3008: else hstepm=estepm;
3009: /* We compute the life expectancy from trapezoids spaced every estepm months
3010: * This is mainly to measure the difference between two models: for example
3011: * if stepm=24 months pijx are given only every 2 years and by summing them
3012: * we are calculating an estimate of the Life Expectancy assuming a linear
3013: * progression in between and thus overestimating or underestimating according
3014: * to the curvature of the survival function. If, for the same date, we
3015: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3016: * to compare the new estimate of Life expectancy with the same linear
3017: * hypothesis. A more precise result, taking into account a more precise
3018: * curvature will be obtained if estepm is as small as stepm. */
3019:
3020: /* For example we decided to compute the life expectancy with the smallest unit */
3021: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3022: nhstepm is the number of hstepm from age to agelim
3023: nstepm is the number of stepm from age to agelin.
3024: Look at hpijx to understand the reason of that which relies in memory size
3025: and note for a fixed period like estepm months */
3026: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3027: survival function given by stepm (the optimization length). Unfortunately it
3028: means that if the survival funtion is printed only each two years of age and if
3029: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3030: results. So we changed our mind and took the option of the best precision.
3031: */
3032: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3033:
3034: /* If stepm=6 months */
3035: /* nhstepm age range expressed in number of stepm */
3036: agelim=AGESUP;
3037: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3038: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3039: /* if (stepm >= YEARM) hstepm=1;*/
3040: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3041:
3042: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3043: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3044: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3045: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3046: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3047: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3048:
3049: for (age=bage; age<=fage; age ++){
3050: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3051: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3052: /* if (stepm >= YEARM) hstepm=1;*/
3053: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3054:
3055: /* If stepm=6 months */
3056: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3057: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3058:
3059: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3060:
3061: /* Computing Variances of health expectancies */
3062: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3063: decrease memory allocation */
3064: for(theta=1; theta <=npar; theta++){
3065: for(i=1; i<=npar; i++){
3066: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3067: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3068: }
3069: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3070: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3071:
3072: for(j=1; j<= nlstate; j++){
3073: for(i=1; i<=nlstate; i++){
3074: for(h=0; h<=nhstepm-1; h++){
3075: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3076: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3077: }
3078: }
3079: }
3080:
3081: for(ij=1; ij<= nlstate*nlstate; ij++)
3082: for(h=0; h<=nhstepm-1; h++){
3083: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3084: }
3085: }/* End theta */
3086:
3087:
3088: for(h=0; h<=nhstepm-1; h++)
3089: for(j=1; j<=nlstate*nlstate;j++)
3090: for(theta=1; theta <=npar; theta++)
3091: trgradg[h][j][theta]=gradg[h][theta][j];
3092:
3093:
3094: for(ij=1;ij<=nlstate*nlstate;ij++)
3095: for(ji=1;ji<=nlstate*nlstate;ji++)
3096: varhe[ij][ji][(int)age] =0.;
3097:
3098: printf("%d|",(int)age);fflush(stdout);
3099: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3100: for(h=0;h<=nhstepm-1;h++){
3101: for(k=0;k<=nhstepm-1;k++){
3102: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3103: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3104: for(ij=1;ij<=nlstate*nlstate;ij++)
3105: for(ji=1;ji<=nlstate*nlstate;ji++)
3106: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3107: }
3108: }
3109:
3110: /* Computing expectancies */
3111: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3112: for(i=1; i<=nlstate;i++)
3113: for(j=1; j<=nlstate;j++)
3114: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3115: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3116:
3117: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
3118:
3119: }
3120:
3121: fprintf(ficresstdeij,"%3.0f",age );
3122: for(i=1; i<=nlstate;i++){
3123: eip=0.;
3124: vip=0.;
3125: for(j=1; j<=nlstate;j++){
3126: eip += eij[i][j][(int)age];
3127: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3128: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3129: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3130: }
3131: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3132: }
3133: fprintf(ficresstdeij,"\n");
3134:
3135: fprintf(ficrescveij,"%3.0f",age );
3136: for(i=1; i<=nlstate;i++)
3137: for(j=1; j<=nlstate;j++){
3138: cptj= (j-1)*nlstate+i;
3139: for(i2=1; i2<=nlstate;i2++)
3140: for(j2=1; j2<=nlstate;j2++){
3141: cptj2= (j2-1)*nlstate+i2;
3142: if(cptj2 <= cptj)
3143: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3144: }
3145: }
3146: fprintf(ficrescveij,"\n");
3147:
3148: }
3149: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3150: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3151: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3152: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3153: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3154: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3155: printf("\n");
3156: fprintf(ficlog,"\n");
3157:
3158: free_vector(xm,1,npar);
3159: free_vector(xp,1,npar);
3160: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3161: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3162: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3163: }
3164:
3165: /************ Variance ******************/
3166: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
3167: {
3168: /* Variance of health expectancies */
3169: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3170: /* double **newm;*/
3171: double **dnewm,**doldm;
3172: double **dnewmp,**doldmp;
3173: int i, j, nhstepm, hstepm, h, nstepm ;
3174: int k, cptcode;
3175: double *xp;
3176: double **gp, **gm; /* for var eij */
3177: double ***gradg, ***trgradg; /*for var eij */
3178: double **gradgp, **trgradgp; /* for var p point j */
3179: double *gpp, *gmp; /* for var p point j */
3180: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3181: double ***p3mat;
3182: double age,agelim, hf;
3183: double ***mobaverage;
3184: int theta;
3185: char digit[4];
3186: char digitp[25];
3187:
3188: char fileresprobmorprev[FILENAMELENGTH];
3189:
3190: if(popbased==1){
3191: if(mobilav!=0)
3192: strcpy(digitp,"-populbased-mobilav-");
3193: else strcpy(digitp,"-populbased-nomobil-");
3194: }
3195: else
3196: strcpy(digitp,"-stablbased-");
3197:
3198: if (mobilav!=0) {
3199: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3200: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3201: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3202: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3203: }
3204: }
3205:
3206: strcpy(fileresprobmorprev,"prmorprev");
3207: sprintf(digit,"%-d",ij);
3208: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3209: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3210: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3211: strcat(fileresprobmorprev,fileres);
3212: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3213: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3214: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3215: }
3216: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3217:
3218: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3219: pstamp(ficresprobmorprev);
3220: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
3221: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3222: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3223: fprintf(ficresprobmorprev," p.%-d SE",j);
3224: for(i=1; i<=nlstate;i++)
3225: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3226: }
3227: fprintf(ficresprobmorprev,"\n");
3228: fprintf(ficgp,"\n# Routine varevsij");
3229: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3230: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
3231: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3232: /* } */
3233: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3234: pstamp(ficresvij);
3235: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3236: if(popbased==1)
3237: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
3238: else
3239: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3240: fprintf(ficresvij,"# Age");
3241: for(i=1; i<=nlstate;i++)
3242: for(j=1; j<=nlstate;j++)
3243: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3244: fprintf(ficresvij,"\n");
3245:
3246: xp=vector(1,npar);
3247: dnewm=matrix(1,nlstate,1,npar);
3248: doldm=matrix(1,nlstate,1,nlstate);
3249: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3250: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3251:
3252: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3253: gpp=vector(nlstate+1,nlstate+ndeath);
3254: gmp=vector(nlstate+1,nlstate+ndeath);
3255: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3256:
3257: if(estepm < stepm){
3258: printf ("Problem %d lower than %d\n",estepm, stepm);
3259: }
3260: else hstepm=estepm;
3261: /* For example we decided to compute the life expectancy with the smallest unit */
3262: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3263: nhstepm is the number of hstepm from age to agelim
3264: nstepm is the number of stepm from age to agelin.
3265: Look at function hpijx to understand why (it is linked to memory size questions) */
3266: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3267: survival function given by stepm (the optimization length). Unfortunately it
3268: means that if the survival funtion is printed every two years of age and if
3269: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3270: results. So we changed our mind and took the option of the best precision.
3271: */
3272: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3273: agelim = AGESUP;
3274: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3275: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3276: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3277: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3278: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3279: gp=matrix(0,nhstepm,1,nlstate);
3280: gm=matrix(0,nhstepm,1,nlstate);
3281:
3282:
3283: for(theta=1; theta <=npar; theta++){
3284: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3285: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3286: }
3287: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3288: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3289:
3290: if (popbased==1) {
3291: if(mobilav ==0){
3292: for(i=1; i<=nlstate;i++)
3293: prlim[i][i]=probs[(int)age][i][ij];
3294: }else{ /* mobilav */
3295: for(i=1; i<=nlstate;i++)
3296: prlim[i][i]=mobaverage[(int)age][i][ij];
3297: }
3298: }
3299:
3300: for(j=1; j<= nlstate; j++){
3301: for(h=0; h<=nhstepm; h++){
3302: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3303: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3304: }
3305: }
3306: /* This for computing probability of death (h=1 means
3307: computed over hstepm matrices product = hstepm*stepm months)
3308: as a weighted average of prlim.
3309: */
3310: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3311: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3312: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3313: }
3314: /* end probability of death */
3315:
3316: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3317: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3318: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3319: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3320:
3321: if (popbased==1) {
3322: if(mobilav ==0){
3323: for(i=1; i<=nlstate;i++)
3324: prlim[i][i]=probs[(int)age][i][ij];
3325: }else{ /* mobilav */
3326: for(i=1; i<=nlstate;i++)
3327: prlim[i][i]=mobaverage[(int)age][i][ij];
3328: }
3329: }
3330:
3331: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3332: for(h=0; h<=nhstepm; h++){
3333: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3334: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3335: }
3336: }
3337: /* This for computing probability of death (h=1 means
3338: computed over hstepm matrices product = hstepm*stepm months)
3339: as a weighted average of prlim.
3340: */
3341: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3342: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3343: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3344: }
3345: /* end probability of death */
3346:
3347: for(j=1; j<= nlstate; j++) /* vareij */
3348: for(h=0; h<=nhstepm; h++){
3349: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3350: }
3351:
3352: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3353: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3354: }
3355:
3356: } /* End theta */
3357:
3358: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3359:
3360: for(h=0; h<=nhstepm; h++) /* veij */
3361: for(j=1; j<=nlstate;j++)
3362: for(theta=1; theta <=npar; theta++)
3363: trgradg[h][j][theta]=gradg[h][theta][j];
3364:
3365: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3366: for(theta=1; theta <=npar; theta++)
3367: trgradgp[j][theta]=gradgp[theta][j];
3368:
3369:
3370: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3371: for(i=1;i<=nlstate;i++)
3372: for(j=1;j<=nlstate;j++)
3373: vareij[i][j][(int)age] =0.;
3374:
3375: for(h=0;h<=nhstepm;h++){
3376: for(k=0;k<=nhstepm;k++){
3377: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3378: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3379: for(i=1;i<=nlstate;i++)
3380: for(j=1;j<=nlstate;j++)
3381: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3382: }
3383: }
3384:
3385: /* pptj */
3386: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3387: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3388: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3389: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3390: varppt[j][i]=doldmp[j][i];
3391: /* end ppptj */
3392: /* x centered again */
3393: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3394: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3395:
3396: if (popbased==1) {
3397: if(mobilav ==0){
3398: for(i=1; i<=nlstate;i++)
3399: prlim[i][i]=probs[(int)age][i][ij];
3400: }else{ /* mobilav */
3401: for(i=1; i<=nlstate;i++)
3402: prlim[i][i]=mobaverage[(int)age][i][ij];
3403: }
3404: }
3405:
3406: /* This for computing probability of death (h=1 means
3407: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3408: as a weighted average of prlim.
3409: */
3410: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3411: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3412: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3413: }
3414: /* end probability of death */
3415:
3416: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3417: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3418: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3419: for(i=1; i<=nlstate;i++){
3420: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3421: }
3422: }
3423: fprintf(ficresprobmorprev,"\n");
3424:
3425: fprintf(ficresvij,"%.0f ",age );
3426: for(i=1; i<=nlstate;i++)
3427: for(j=1; j<=nlstate;j++){
3428: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3429: }
3430: fprintf(ficresvij,"\n");
3431: free_matrix(gp,0,nhstepm,1,nlstate);
3432: free_matrix(gm,0,nhstepm,1,nlstate);
3433: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3434: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3435: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3436: } /* End age */
3437: free_vector(gpp,nlstate+1,nlstate+ndeath);
3438: free_vector(gmp,nlstate+1,nlstate+ndeath);
3439: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3440: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3441: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3442: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3443: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3444: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3445: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3446: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3447: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3448: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3449: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3450: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3451: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3452: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
3453: */
3454: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3455: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3456:
3457: free_vector(xp,1,npar);
3458: free_matrix(doldm,1,nlstate,1,nlstate);
3459: free_matrix(dnewm,1,nlstate,1,npar);
3460: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3461: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3462: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3463: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3464: fclose(ficresprobmorprev);
3465: fflush(ficgp);
3466: fflush(fichtm);
3467: } /* end varevsij */
3468:
3469: /************ Variance of prevlim ******************/
3470: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
3471: {
3472: /* Variance of prevalence limit */
3473: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3474: double **newm;
3475: double **dnewm,**doldm;
3476: int i, j, nhstepm, hstepm;
3477: int k, cptcode;
3478: double *xp;
3479: double *gp, *gm;
3480: double **gradg, **trgradg;
3481: double age,agelim;
3482: int theta;
3483:
3484: pstamp(ficresvpl);
3485: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3486: fprintf(ficresvpl,"# Age");
3487: for(i=1; i<=nlstate;i++)
3488: fprintf(ficresvpl," %1d-%1d",i,i);
3489: fprintf(ficresvpl,"\n");
3490:
3491: xp=vector(1,npar);
3492: dnewm=matrix(1,nlstate,1,npar);
3493: doldm=matrix(1,nlstate,1,nlstate);
3494:
3495: hstepm=1*YEARM; /* Every year of age */
3496: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3497: agelim = AGESUP;
3498: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3499: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3500: if (stepm >= YEARM) hstepm=1;
3501: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3502: gradg=matrix(1,npar,1,nlstate);
3503: gp=vector(1,nlstate);
3504: gm=vector(1,nlstate);
3505:
3506: for(theta=1; theta <=npar; theta++){
3507: for(i=1; i<=npar; i++){ /* Computes gradient */
3508: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3509: }
3510: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3511: for(i=1;i<=nlstate;i++)
3512: gp[i] = prlim[i][i];
3513:
3514: for(i=1; i<=npar; i++) /* Computes gradient */
3515: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3516: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3517: for(i=1;i<=nlstate;i++)
3518: gm[i] = prlim[i][i];
3519:
3520: for(i=1;i<=nlstate;i++)
3521: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3522: } /* End theta */
3523:
3524: trgradg =matrix(1,nlstate,1,npar);
3525:
3526: for(j=1; j<=nlstate;j++)
3527: for(theta=1; theta <=npar; theta++)
3528: trgradg[j][theta]=gradg[theta][j];
3529:
3530: for(i=1;i<=nlstate;i++)
3531: varpl[i][(int)age] =0.;
3532: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3533: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3534: for(i=1;i<=nlstate;i++)
3535: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3536:
3537: fprintf(ficresvpl,"%.0f ",age );
3538: for(i=1; i<=nlstate;i++)
3539: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3540: fprintf(ficresvpl,"\n");
3541: free_vector(gp,1,nlstate);
3542: free_vector(gm,1,nlstate);
3543: free_matrix(gradg,1,npar,1,nlstate);
3544: free_matrix(trgradg,1,nlstate,1,npar);
3545: } /* End age */
3546:
3547: free_vector(xp,1,npar);
3548: free_matrix(doldm,1,nlstate,1,npar);
3549: free_matrix(dnewm,1,nlstate,1,nlstate);
3550:
3551: }
3552:
3553: /************ Variance of one-step probabilities ******************/
3554: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
3555: {
3556: int i, j=0, i1, k1, l1, t, tj;
3557: int k2, l2, j1, z1;
3558: int k=0,l, cptcode;
3559: int first=1, first1, first2;
3560: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3561: double **dnewm,**doldm;
3562: double *xp;
3563: double *gp, *gm;
3564: double **gradg, **trgradg;
3565: double **mu;
3566: double age,agelim, cov[NCOVMAX+1];
3567: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3568: int theta;
3569: char fileresprob[FILENAMELENGTH];
3570: char fileresprobcov[FILENAMELENGTH];
3571: char fileresprobcor[FILENAMELENGTH];
3572: double ***varpij;
3573:
3574: strcpy(fileresprob,"prob");
3575: strcat(fileresprob,fileres);
3576: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3577: printf("Problem with resultfile: %s\n", fileresprob);
3578: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3579: }
3580: strcpy(fileresprobcov,"probcov");
3581: strcat(fileresprobcov,fileres);
3582: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3583: printf("Problem with resultfile: %s\n", fileresprobcov);
3584: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3585: }
3586: strcpy(fileresprobcor,"probcor");
3587: strcat(fileresprobcor,fileres);
3588: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3589: printf("Problem with resultfile: %s\n", fileresprobcor);
3590: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3591: }
3592: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3593: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3594: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3595: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3596: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3597: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3598: pstamp(ficresprob);
3599: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3600: fprintf(ficresprob,"# Age");
3601: pstamp(ficresprobcov);
3602: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3603: fprintf(ficresprobcov,"# Age");
3604: pstamp(ficresprobcor);
3605: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3606: fprintf(ficresprobcor,"# Age");
3607:
3608:
3609: for(i=1; i<=nlstate;i++)
3610: for(j=1; j<=(nlstate+ndeath);j++){
3611: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3612: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3613: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3614: }
3615: /* fprintf(ficresprob,"\n");
3616: fprintf(ficresprobcov,"\n");
3617: fprintf(ficresprobcor,"\n");
3618: */
3619: xp=vector(1,npar);
3620: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3621: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3622: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3623: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3624: first=1;
3625: fprintf(ficgp,"\n# Routine varprob");
3626: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3627: fprintf(fichtm,"\n");
3628:
3629: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3630: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3631: file %s<br>\n",optionfilehtmcov);
3632: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3633: and drawn. It helps understanding how is the covariance between two incidences.\
3634: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3635: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
3636: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3637: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3638: standard deviations wide on each axis. <br>\
3639: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3640: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3641: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3642:
3643: cov[1]=1;
3644: /* tj=cptcoveff; */
3645: tj = (int) pow(2,cptcoveff);
3646: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3647: j1=0;
3648: for(j1=1; j1<=tj;j1++){
3649: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3650: /*j1++;*/
3651: if (cptcovn>0) {
3652: fprintf(ficresprob, "\n#********** Variable ");
3653: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3654: fprintf(ficresprob, "**********\n#\n");
3655: fprintf(ficresprobcov, "\n#********** Variable ");
3656: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3657: fprintf(ficresprobcov, "**********\n#\n");
3658:
3659: fprintf(ficgp, "\n#********** Variable ");
3660: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3661: fprintf(ficgp, "**********\n#\n");
3662:
3663:
3664: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3665: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3666: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3667:
3668: fprintf(ficresprobcor, "\n#********** Variable ");
3669: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3670: fprintf(ficresprobcor, "**********\n#");
3671: }
3672:
3673: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3674: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3675: gp=vector(1,(nlstate)*(nlstate+ndeath));
3676: gm=vector(1,(nlstate)*(nlstate+ndeath));
3677: for (age=bage; age<=fage; age ++){
3678: cov[2]=age;
3679: for (k=1; k<=cptcovn;k++) {
3680: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3681: * 1 1 1 1 1
3682: * 2 2 1 1 1
3683: * 3 1 2 1 1
3684: */
3685: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3686: }
3687: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3688: for (k=1; k<=cptcovprod;k++)
3689: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3690:
3691:
3692: for(theta=1; theta <=npar; theta++){
3693: for(i=1; i<=npar; i++)
3694: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3695:
3696: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3697:
3698: k=0;
3699: for(i=1; i<= (nlstate); i++){
3700: for(j=1; j<=(nlstate+ndeath);j++){
3701: k=k+1;
3702: gp[k]=pmmij[i][j];
3703: }
3704: }
3705:
3706: for(i=1; i<=npar; i++)
3707: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3708:
3709: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3710: k=0;
3711: for(i=1; i<=(nlstate); i++){
3712: for(j=1; j<=(nlstate+ndeath);j++){
3713: k=k+1;
3714: gm[k]=pmmij[i][j];
3715: }
3716: }
3717:
3718: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3719: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3720: }
3721:
3722: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3723: for(theta=1; theta <=npar; theta++)
3724: trgradg[j][theta]=gradg[theta][j];
3725:
3726: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3727: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3728:
3729: pmij(pmmij,cov,ncovmodel,x,nlstate);
3730:
3731: k=0;
3732: for(i=1; i<=(nlstate); i++){
3733: for(j=1; j<=(nlstate+ndeath);j++){
3734: k=k+1;
3735: mu[k][(int) age]=pmmij[i][j];
3736: }
3737: }
3738: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3739: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3740: varpij[i][j][(int)age] = doldm[i][j];
3741:
3742: /*printf("\n%d ",(int)age);
3743: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3744: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3745: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3746: }*/
3747:
3748: fprintf(ficresprob,"\n%d ",(int)age);
3749: fprintf(ficresprobcov,"\n%d ",(int)age);
3750: fprintf(ficresprobcor,"\n%d ",(int)age);
3751:
3752: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3753: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3754: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3755: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3756: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3757: }
3758: i=0;
3759: for (k=1; k<=(nlstate);k++){
3760: for (l=1; l<=(nlstate+ndeath);l++){
3761: i++;
3762: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3763: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3764: for (j=1; j<=i;j++){
3765: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3766: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3767: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3768: }
3769: }
3770: }/* end of loop for state */
3771: } /* end of loop for age */
3772: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3773: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3774: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3775: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3776:
3777: /* Confidence intervalle of pij */
3778: /*
3779: fprintf(ficgp,"\nunset parametric;unset label");
3780: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3781: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3782: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
3783: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3784: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3785: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3786: */
3787:
3788: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3789: first1=1;first2=2;
3790: for (k2=1; k2<=(nlstate);k2++){
3791: for (l2=1; l2<=(nlstate+ndeath);l2++){
3792: if(l2==k2) continue;
3793: j=(k2-1)*(nlstate+ndeath)+l2;
3794: for (k1=1; k1<=(nlstate);k1++){
3795: for (l1=1; l1<=(nlstate+ndeath);l1++){
3796: if(l1==k1) continue;
3797: i=(k1-1)*(nlstate+ndeath)+l1;
3798: if(i<=j) continue;
3799: for (age=bage; age<=fage; age ++){
3800: if ((int)age %5==0){
3801: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3802: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3803: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3804: mu1=mu[i][(int) age]/stepm*YEARM ;
3805: mu2=mu[j][(int) age]/stepm*YEARM;
3806: c12=cv12/sqrt(v1*v2);
3807: /* Computing eigen value of matrix of covariance */
3808: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3809: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3810: if ((lc2 <0) || (lc1 <0) ){
3811: if(first2==1){
3812: first1=0;
3813: printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3814: }
3815: fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
3816: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3817: /* lc2=fabs(lc2); */
3818: }
3819:
3820: /* Eigen vectors */
3821: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3822: /*v21=sqrt(1.-v11*v11); *//* error */
3823: v21=(lc1-v1)/cv12*v11;
3824: v12=-v21;
3825: v22=v11;
3826: tnalp=v21/v11;
3827: if(first1==1){
3828: first1=0;
3829: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
3830: }
3831: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
3832: /*printf(fignu*/
3833: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3834: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3835: if(first==1){
3836: first=0;
3837: fprintf(ficgp,"\nset parametric;unset label");
3838: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
3839: fprintf(ficgp,"\nset ter png small size 320, 240");
3840: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3841: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3842: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3843: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3844: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3845: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3846: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3847: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3848: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3849: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3850: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
3851: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3852: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3853: }else{
3854: first=0;
3855: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3856: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3857: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3858: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
3859: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3860: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3861: }/* if first */
3862: } /* age mod 5 */
3863: } /* end loop age */
3864: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3865: first=1;
3866: } /*l12 */
3867: } /* k12 */
3868: } /*l1 */
3869: }/* k1 */
3870: /* } /* loop covariates */
3871: }
3872: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3873: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3874: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3875: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3876: free_vector(xp,1,npar);
3877: fclose(ficresprob);
3878: fclose(ficresprobcov);
3879: fclose(ficresprobcor);
3880: fflush(ficgp);
3881: fflush(fichtmcov);
3882: }
3883:
3884:
3885: /******************* Printing html file ***********/
3886: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3887: int lastpass, int stepm, int weightopt, char model[],\
3888: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3889: int popforecast, int estepm ,\
3890: double jprev1, double mprev1,double anprev1, \
3891: double jprev2, double mprev2,double anprev2){
3892: int jj1, k1, i1, cpt;
3893:
3894: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3895: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3896: </ul>");
3897: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3898: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3899: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3900: fprintf(fichtm,"\
3901: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3902: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3903: fprintf(fichtm,"\
3904: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3905: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3906: fprintf(fichtm,"\
3907: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
3908: <a href=\"%s\">%s</a> <br>\n",
3909: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3910: fprintf(fichtm,"\
3911: - Population projections by age and states: \
3912: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3913:
3914: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3915:
3916: m=pow(2,cptcoveff);
3917: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3918:
3919: jj1=0;
3920: for(k1=1; k1<=m;k1++){
3921: for(i1=1; i1<=ncodemax[k1];i1++){
3922: jj1++;
3923: if (cptcovn > 0) {
3924: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3925: for (cpt=1; cpt<=cptcoveff;cpt++)
3926: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3927: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3928: }
3929: /* Pij */
3930: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
3931: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3932: /* Quasi-incidences */
3933: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3934: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
3935: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3936: /* Period (stable) prevalence in each health state */
3937: for(cpt=1; cpt<=nlstate;cpt++){
3938: fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3939: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3940: }
3941: for(cpt=1; cpt<=nlstate;cpt++) {
3942: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3943: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3944: }
3945: } /* end i1 */
3946: }/* End k1 */
3947: fprintf(fichtm,"</ul>");
3948:
3949:
3950: fprintf(fichtm,"\
3951: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3952: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3953:
3954: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3955: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3956: fprintf(fichtm,"\
3957: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3958: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3959:
3960: fprintf(fichtm,"\
3961: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3962: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3963: fprintf(fichtm,"\
3964: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
3965: <a href=\"%s\">%s</a> <br>\n</li>",
3966: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3967: fprintf(fichtm,"\
3968: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
3969: <a href=\"%s\">%s</a> <br>\n</li>",
3970: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3971: fprintf(fichtm,"\
3972: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3973: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3974: fprintf(fichtm,"\
3975: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
3976: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3977: fprintf(fichtm,"\
3978: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3979: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3980:
3981: /* if(popforecast==1) fprintf(fichtm,"\n */
3982: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3983: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3984: /* <br>",fileres,fileres,fileres,fileres); */
3985: /* else */
3986: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
3987: fflush(fichtm);
3988: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3989:
3990: m=pow(2,cptcoveff);
3991: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3992:
3993: jj1=0;
3994: for(k1=1; k1<=m;k1++){
3995: for(i1=1; i1<=ncodemax[k1];i1++){
3996: jj1++;
3997: if (cptcovn > 0) {
3998: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3999: for (cpt=1; cpt<=cptcoveff;cpt++)
4000: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4001: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4002: }
4003: for(cpt=1; cpt<=nlstate;cpt++) {
4004: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4005: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4006: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4007: }
4008: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4009: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4010: true period expectancies (those weighted with period prevalences are also\
4011: drawn in addition to the population based expectancies computed using\
4012: observed and cahotic prevalences: %s%d.png<br>\
4013: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4014: } /* end i1 */
4015: }/* End k1 */
4016: fprintf(fichtm,"</ul>");
4017: fflush(fichtm);
4018: }
4019:
4020: /******************* Gnuplot file **************/
4021: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4022:
4023: char dirfileres[132],optfileres[132];
4024: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4025: int ng=0;
4026: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4027: /* printf("Problem with file %s",optionfilegnuplot); */
4028: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4029: /* } */
4030:
4031: /*#ifdef windows */
4032: fprintf(ficgp,"cd \"%s\" \n",pathc);
4033: /*#endif */
4034: m=pow(2,cptcoveff);
4035:
4036: strcpy(dirfileres,optionfilefiname);
4037: strcpy(optfileres,"vpl");
4038: /* 1eme*/
4039: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4040: for (cpt=1; cpt<= nlstate ; cpt ++) {
4041: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4042: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4043: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4044: fprintf(ficgp,"set xlabel \"Age\" \n\
4045: set ylabel \"Probability\" \n\
4046: set ter png small size 320, 240\n\
4047: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4048:
4049: for (i=1; i<= nlstate ; i ++) {
4050: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4051: else fprintf(ficgp," \%%*lf (\%%*lf)");
4052: }
4053: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4054: for (i=1; i<= nlstate ; i ++) {
4055: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4056: else fprintf(ficgp," \%%*lf (\%%*lf)");
4057: }
4058: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4059: for (i=1; i<= nlstate ; i ++) {
4060: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4061: else fprintf(ficgp," \%%*lf (\%%*lf)");
4062: }
4063: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4064: }
4065: }
4066: /*2 eme*/
4067: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4068: for (k1=1; k1<= m ; k1 ++) {
4069: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4070: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4071:
4072: for (i=1; i<= nlstate+1 ; i ++) {
4073: k=2*i;
4074: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4075: for (j=1; j<= nlstate+1 ; j ++) {
4076: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4077: else fprintf(ficgp," \%%*lf (\%%*lf)");
4078: }
4079: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4080: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4081: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4082: for (j=1; j<= nlstate+1 ; j ++) {
4083: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4084: else fprintf(ficgp," \%%*lf (\%%*lf)");
4085: }
4086: fprintf(ficgp,"\" t\"\" w l lt 0,");
4087: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4088: for (j=1; j<= nlstate+1 ; j ++) {
4089: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4090: else fprintf(ficgp," \%%*lf (\%%*lf)");
4091: }
4092: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4093: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4094: }
4095: }
4096:
4097: /*3eme*/
4098:
4099: for (k1=1; k1<= m ; k1 ++) {
4100: for (cpt=1; cpt<= nlstate ; cpt ++) {
4101: /* k=2+nlstate*(2*cpt-2); */
4102: k=2+(nlstate+1)*(cpt-1);
4103: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4104: fprintf(ficgp,"set ter png small size 320, 240\n\
4105: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4106: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4107: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4108: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4109: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4110: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4111: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4112:
4113: */
4114: for (i=1; i< nlstate ; i ++) {
4115: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
4116: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
4117:
4118: }
4119: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4120: }
4121: }
4122:
4123: /* CV preval stable (period) */
4124: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4125: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4126: k=3;
4127: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4128: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4129: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4130: set ter png small size 320, 240\n\
4131: unset log y\n\
4132: plot [%.f:%.f] ", ageminpar, agemaxpar);
4133: for (i=1; i<= nlstate ; i ++){
4134: if(i==1)
4135: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4136: else
4137: fprintf(ficgp,", '' ");
4138: l=(nlstate+ndeath)*(i-1)+1;
4139: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4140: for (j=1; j<= (nlstate-1) ; j ++)
4141: fprintf(ficgp,"+$%d",k+l+j);
4142: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4143: } /* nlstate */
4144: fprintf(ficgp,"\n");
4145: } /* end cpt state*/
4146: } /* end covariate */
4147:
4148: /* proba elementaires */
4149: for(i=1,jk=1; i <=nlstate; i++){
4150: for(k=1; k <=(nlstate+ndeath); k++){
4151: if (k != i) {
4152: for(j=1; j <=ncovmodel; j++){
4153: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4154: jk++;
4155: fprintf(ficgp,"\n");
4156: }
4157: }
4158: }
4159: }
4160: /*goto avoid;*/
4161: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4162: for(jk=1; jk <=m; jk++) {
4163: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4164: if (ng==2)
4165: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4166: else
4167: fprintf(ficgp,"\nset title \"Probability\"\n");
4168: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4169: i=1;
4170: for(k2=1; k2<=nlstate; k2++) {
4171: k3=i;
4172: for(k=1; k<=(nlstate+ndeath); k++) {
4173: if (k != k2){
4174: if(ng==2)
4175: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4176: else
4177: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4178: ij=1;/* To be checked else nbcode[0][0] wrong */
4179: for(j=3; j <=ncovmodel; j++) {
4180: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4181: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4182: /* ij++; */
4183: /* } */
4184: /* else */
4185: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4186: }
4187: fprintf(ficgp,")/(1");
4188:
4189: for(k1=1; k1 <=nlstate; k1++){
4190: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4191: ij=1;
4192: for(j=3; j <=ncovmodel; j++){
4193: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4194: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4195: /* ij++; */
4196: /* } */
4197: /* else */
4198: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4199: }
4200: fprintf(ficgp,")");
4201: }
4202: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4203: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4204: i=i+ncovmodel;
4205: }
4206: } /* end k */
4207: } /* end k2 */
4208: } /* end jk */
4209: } /* end ng */
4210: avoid:
4211: fflush(ficgp);
4212: } /* end gnuplot */
4213:
4214:
4215: /*************** Moving average **************/
4216: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4217:
4218: int i, cpt, cptcod;
4219: int modcovmax =1;
4220: int mobilavrange, mob;
4221: double age;
4222:
4223: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4224: a covariate has 2 modalities */
4225: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4226:
4227: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4228: if(mobilav==1) mobilavrange=5; /* default */
4229: else mobilavrange=mobilav;
4230: for (age=bage; age<=fage; age++)
4231: for (i=1; i<=nlstate;i++)
4232: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4233: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4234: /* We keep the original values on the extreme ages bage, fage and for
4235: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4236: we use a 5 terms etc. until the borders are no more concerned.
4237: */
4238: for (mob=3;mob <=mobilavrange;mob=mob+2){
4239: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4240: for (i=1; i<=nlstate;i++){
4241: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4242: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4243: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4244: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4245: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4246: }
4247: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4248: }
4249: }
4250: }/* end age */
4251: }/* end mob */
4252: }else return -1;
4253: return 0;
4254: }/* End movingaverage */
4255:
4256:
4257: /************** Forecasting ******************/
4258: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
4259: /* proj1, year, month, day of starting projection
4260: agemin, agemax range of age
4261: dateprev1 dateprev2 range of dates during which prevalence is computed
4262: anproj2 year of en of projection (same day and month as proj1).
4263: */
4264: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4265: int *popage;
4266: double agec; /* generic age */
4267: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4268: double *popeffectif,*popcount;
4269: double ***p3mat;
4270: double ***mobaverage;
4271: char fileresf[FILENAMELENGTH];
4272:
4273: agelim=AGESUP;
4274: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4275:
4276: strcpy(fileresf,"f");
4277: strcat(fileresf,fileres);
4278: if((ficresf=fopen(fileresf,"w"))==NULL) {
4279: printf("Problem with forecast resultfile: %s\n", fileresf);
4280: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4281: }
4282: printf("Computing forecasting: result on file '%s' \n", fileresf);
4283: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4284:
4285: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4286:
4287: if (mobilav!=0) {
4288: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4289: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4290: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4291: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4292: }
4293: }
4294:
4295: stepsize=(int) (stepm+YEARM-1)/YEARM;
4296: if (stepm<=12) stepsize=1;
4297: if(estepm < stepm){
4298: printf ("Problem %d lower than %d\n",estepm, stepm);
4299: }
4300: else hstepm=estepm;
4301:
4302: hstepm=hstepm/stepm;
4303: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4304: fractional in yp1 */
4305: anprojmean=yp;
4306: yp2=modf((yp1*12),&yp);
4307: mprojmean=yp;
4308: yp1=modf((yp2*30.5),&yp);
4309: jprojmean=yp;
4310: if(jprojmean==0) jprojmean=1;
4311: if(mprojmean==0) jprojmean=1;
4312:
4313: i1=cptcoveff;
4314: if (cptcovn < 1){i1=1;}
4315:
4316: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4317:
4318: fprintf(ficresf,"#****** Routine prevforecast **\n");
4319:
4320: /* if (h==(int)(YEARM*yearp)){ */
4321: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4322: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4323: k=k+1;
4324: fprintf(ficresf,"\n#******");
4325: for(j=1;j<=cptcoveff;j++) {
4326: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4327: }
4328: fprintf(ficresf,"******\n");
4329: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4330: for(j=1; j<=nlstate+ndeath;j++){
4331: for(i=1; i<=nlstate;i++)
4332: fprintf(ficresf," p%d%d",i,j);
4333: fprintf(ficresf," p.%d",j);
4334: }
4335: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4336: fprintf(ficresf,"\n");
4337: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4338:
4339: for (agec=fage; agec>=(ageminpar-1); agec--){
4340: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4341: nhstepm = nhstepm/hstepm;
4342: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4343: oldm=oldms;savm=savms;
4344: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4345:
4346: for (h=0; h<=nhstepm; h++){
4347: if (h*hstepm/YEARM*stepm ==yearp) {
4348: fprintf(ficresf,"\n");
4349: for(j=1;j<=cptcoveff;j++)
4350: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4351: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4352: }
4353: for(j=1; j<=nlstate+ndeath;j++) {
4354: ppij=0.;
4355: for(i=1; i<=nlstate;i++) {
4356: if (mobilav==1)
4357: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4358: else {
4359: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4360: }
4361: if (h*hstepm/YEARM*stepm== yearp) {
4362: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4363: }
4364: } /* end i */
4365: if (h*hstepm/YEARM*stepm==yearp) {
4366: fprintf(ficresf," %.3f", ppij);
4367: }
4368: }/* end j */
4369: } /* end h */
4370: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4371: } /* end agec */
4372: } /* end yearp */
4373: } /* end cptcod */
4374: } /* end cptcov */
4375:
4376: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4377:
4378: fclose(ficresf);
4379: }
4380:
4381: /************** Forecasting *****not tested NB*************/
4382: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
4383:
4384: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4385: int *popage;
4386: double calagedatem, agelim, kk1, kk2;
4387: double *popeffectif,*popcount;
4388: double ***p3mat,***tabpop,***tabpopprev;
4389: double ***mobaverage;
4390: char filerespop[FILENAMELENGTH];
4391:
4392: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4393: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4394: agelim=AGESUP;
4395: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4396:
4397: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4398:
4399:
4400: strcpy(filerespop,"pop");
4401: strcat(filerespop,fileres);
4402: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4403: printf("Problem with forecast resultfile: %s\n", filerespop);
4404: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4405: }
4406: printf("Computing forecasting: result on file '%s' \n", filerespop);
4407: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4408:
4409: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4410:
4411: if (mobilav!=0) {
4412: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4413: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4414: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4415: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4416: }
4417: }
4418:
4419: stepsize=(int) (stepm+YEARM-1)/YEARM;
4420: if (stepm<=12) stepsize=1;
4421:
4422: agelim=AGESUP;
4423:
4424: hstepm=1;
4425: hstepm=hstepm/stepm;
4426:
4427: if (popforecast==1) {
4428: if((ficpop=fopen(popfile,"r"))==NULL) {
4429: printf("Problem with population file : %s\n",popfile);exit(0);
4430: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4431: }
4432: popage=ivector(0,AGESUP);
4433: popeffectif=vector(0,AGESUP);
4434: popcount=vector(0,AGESUP);
4435:
4436: i=1;
4437: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4438:
4439: imx=i;
4440: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4441: }
4442:
4443: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4444: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4445: k=k+1;
4446: fprintf(ficrespop,"\n#******");
4447: for(j=1;j<=cptcoveff;j++) {
4448: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4449: }
4450: fprintf(ficrespop,"******\n");
4451: fprintf(ficrespop,"# Age");
4452: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4453: if (popforecast==1) fprintf(ficrespop," [Population]");
4454:
4455: for (cpt=0; cpt<=0;cpt++) {
4456: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4457:
4458: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4459: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4460: nhstepm = nhstepm/hstepm;
4461:
4462: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4463: oldm=oldms;savm=savms;
4464: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4465:
4466: for (h=0; h<=nhstepm; h++){
4467: if (h==(int) (calagedatem+YEARM*cpt)) {
4468: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4469: }
4470: for(j=1; j<=nlstate+ndeath;j++) {
4471: kk1=0.;kk2=0;
4472: for(i=1; i<=nlstate;i++) {
4473: if (mobilav==1)
4474: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4475: else {
4476: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4477: }
4478: }
4479: if (h==(int)(calagedatem+12*cpt)){
4480: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4481: /*fprintf(ficrespop," %.3f", kk1);
4482: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4483: }
4484: }
4485: for(i=1; i<=nlstate;i++){
4486: kk1=0.;
4487: for(j=1; j<=nlstate;j++){
4488: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4489: }
4490: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4491: }
4492:
4493: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4494: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4495: }
4496: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4497: }
4498: }
4499:
4500: /******/
4501:
4502: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4503: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4504: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4505: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4506: nhstepm = nhstepm/hstepm;
4507:
4508: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4509: oldm=oldms;savm=savms;
4510: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4511: for (h=0; h<=nhstepm; h++){
4512: if (h==(int) (calagedatem+YEARM*cpt)) {
4513: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4514: }
4515: for(j=1; j<=nlstate+ndeath;j++) {
4516: kk1=0.;kk2=0;
4517: for(i=1; i<=nlstate;i++) {
4518: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4519: }
4520: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4521: }
4522: }
4523: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4524: }
4525: }
4526: }
4527: }
4528:
4529: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4530:
4531: if (popforecast==1) {
4532: free_ivector(popage,0,AGESUP);
4533: free_vector(popeffectif,0,AGESUP);
4534: free_vector(popcount,0,AGESUP);
4535: }
4536: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4537: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4538: fclose(ficrespop);
4539: } /* End of popforecast */
4540:
4541: int fileappend(FILE *fichier, char *optionfich)
4542: {
4543: if((fichier=fopen(optionfich,"a"))==NULL) {
4544: printf("Problem with file: %s\n", optionfich);
4545: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4546: return (0);
4547: }
4548: fflush(fichier);
4549: return (1);
4550: }
4551:
4552:
4553: /**************** function prwizard **********************/
4554: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4555: {
4556:
4557: /* Wizard to print covariance matrix template */
4558:
4559: char ca[32], cb[32], cc[32];
4560: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4561: int numlinepar;
4562:
4563: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4564: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4565: for(i=1; i <=nlstate; i++){
4566: jj=0;
4567: for(j=1; j <=nlstate+ndeath; j++){
4568: if(j==i) continue;
4569: jj++;
4570: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4571: printf("%1d%1d",i,j);
4572: fprintf(ficparo,"%1d%1d",i,j);
4573: for(k=1; k<=ncovmodel;k++){
4574: /* printf(" %lf",param[i][j][k]); */
4575: /* fprintf(ficparo," %lf",param[i][j][k]); */
4576: printf(" 0.");
4577: fprintf(ficparo," 0.");
4578: }
4579: printf("\n");
4580: fprintf(ficparo,"\n");
4581: }
4582: }
4583: printf("# Scales (for hessian or gradient estimation)\n");
4584: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4585: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4586: for(i=1; i <=nlstate; i++){
4587: jj=0;
4588: for(j=1; j <=nlstate+ndeath; j++){
4589: if(j==i) continue;
4590: jj++;
4591: fprintf(ficparo,"%1d%1d",i,j);
4592: printf("%1d%1d",i,j);
4593: fflush(stdout);
4594: for(k=1; k<=ncovmodel;k++){
4595: /* printf(" %le",delti3[i][j][k]); */
4596: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4597: printf(" 0.");
4598: fprintf(ficparo," 0.");
4599: }
4600: numlinepar++;
4601: printf("\n");
4602: fprintf(ficparo,"\n");
4603: }
4604: }
4605: printf("# Covariance matrix\n");
4606: /* # 121 Var(a12)\n\ */
4607: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4608: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4609: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4610: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4611: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4612: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4613: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4614: fflush(stdout);
4615: fprintf(ficparo,"# Covariance matrix\n");
4616: /* # 121 Var(a12)\n\ */
4617: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4618: /* # ...\n\ */
4619: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4620:
4621: for(itimes=1;itimes<=2;itimes++){
4622: jj=0;
4623: for(i=1; i <=nlstate; i++){
4624: for(j=1; j <=nlstate+ndeath; j++){
4625: if(j==i) continue;
4626: for(k=1; k<=ncovmodel;k++){
4627: jj++;
4628: ca[0]= k+'a'-1;ca[1]='\0';
4629: if(itimes==1){
4630: printf("#%1d%1d%d",i,j,k);
4631: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4632: }else{
4633: printf("%1d%1d%d",i,j,k);
4634: fprintf(ficparo,"%1d%1d%d",i,j,k);
4635: /* printf(" %.5le",matcov[i][j]); */
4636: }
4637: ll=0;
4638: for(li=1;li <=nlstate; li++){
4639: for(lj=1;lj <=nlstate+ndeath; lj++){
4640: if(lj==li) continue;
4641: for(lk=1;lk<=ncovmodel;lk++){
4642: ll++;
4643: if(ll<=jj){
4644: cb[0]= lk +'a'-1;cb[1]='\0';
4645: if(ll<jj){
4646: if(itimes==1){
4647: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4648: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4649: }else{
4650: printf(" 0.");
4651: fprintf(ficparo," 0.");
4652: }
4653: }else{
4654: if(itimes==1){
4655: printf(" Var(%s%1d%1d)",ca,i,j);
4656: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4657: }else{
4658: printf(" 0.");
4659: fprintf(ficparo," 0.");
4660: }
4661: }
4662: }
4663: } /* end lk */
4664: } /* end lj */
4665: } /* end li */
4666: printf("\n");
4667: fprintf(ficparo,"\n");
4668: numlinepar++;
4669: } /* end k*/
4670: } /*end j */
4671: } /* end i */
4672: } /* end itimes */
4673:
4674: } /* end of prwizard */
4675: /******************* Gompertz Likelihood ******************************/
4676: double gompertz(double x[])
4677: {
4678: double A,B,L=0.0,sump=0.,num=0.;
4679: int i,n=0; /* n is the size of the sample */
4680:
4681: for (i=0;i<=imx-1 ; i++) {
4682: sump=sump+weight[i];
4683: /* sump=sump+1;*/
4684: num=num+1;
4685: }
4686:
4687:
4688: /* for (i=0; i<=imx; i++)
4689: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
4690:
4691: for (i=1;i<=imx ; i++)
4692: {
4693: if (cens[i] == 1 && wav[i]>1)
4694: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4695:
4696: if (cens[i] == 0 && wav[i]>1)
4697: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4698: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4699:
4700: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4701: if (wav[i] > 1 ) { /* ??? */
4702: L=L+A*weight[i];
4703: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
4704: }
4705: }
4706:
4707: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4708:
4709: return -2*L*num/sump;
4710: }
4711:
4712: #ifdef GSL
4713: /******************* Gompertz_f Likelihood ******************************/
4714: double gompertz_f(const gsl_vector *v, void *params)
4715: {
4716: double A,B,LL=0.0,sump=0.,num=0.;
4717: double *x= (double *) v->data;
4718: int i,n=0; /* n is the size of the sample */
4719:
4720: for (i=0;i<=imx-1 ; i++) {
4721: sump=sump+weight[i];
4722: /* sump=sump+1;*/
4723: num=num+1;
4724: }
4725:
4726:
4727: /* for (i=0; i<=imx; i++)
4728: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
4729: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4730: for (i=1;i<=imx ; i++)
4731: {
4732: if (cens[i] == 1 && wav[i]>1)
4733: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4734:
4735: if (cens[i] == 0 && wav[i]>1)
4736: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4737: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4738:
4739: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4740: if (wav[i] > 1 ) { /* ??? */
4741: LL=LL+A*weight[i];
4742: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
4743: }
4744: }
4745:
4746: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4747: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4748:
4749: return -2*LL*num/sump;
4750: }
4751: #endif
4752:
4753: /******************* Printing html file ***********/
4754: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4755: int lastpass, int stepm, int weightopt, char model[],\
4756: int imx, double p[],double **matcov,double agemortsup){
4757: int i,k;
4758:
4759: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4760: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4761: for (i=1;i<=2;i++)
4762: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4763: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4764: fprintf(fichtm,"</ul>");
4765:
4766: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4767:
4768: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
4769:
4770: for (k=agegomp;k<(agemortsup-2);k++)
4771: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4772:
4773:
4774: fflush(fichtm);
4775: }
4776:
4777: /******************* Gnuplot file **************/
4778: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4779:
4780: char dirfileres[132],optfileres[132];
4781: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4782: int ng;
4783:
4784:
4785: /*#ifdef windows */
4786: fprintf(ficgp,"cd \"%s\" \n",pathc);
4787: /*#endif */
4788:
4789:
4790: strcpy(dirfileres,optionfilefiname);
4791: strcpy(optfileres,"vpl");
4792: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4793: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4794: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4795: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4796: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4797:
4798: }
4799:
4800: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4801: {
4802:
4803: /*-------- data file ----------*/
4804: FILE *fic;
4805: char dummy[]=" ";
4806: int i, j, n;
4807: int linei, month, year,iout;
4808: char line[MAXLINE], linetmp[MAXLINE];
4809: char stra[80], strb[80];
4810: char *stratrunc;
4811: int lstra;
4812:
4813:
4814: if((fic=fopen(datafile,"r"))==NULL) {
4815: printf("Problem while opening datafile: %s\n", datafile);return 1;
4816: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4817: }
4818:
4819: i=1;
4820: linei=0;
4821: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4822: linei=linei+1;
4823: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4824: if(line[j] == '\t')
4825: line[j] = ' ';
4826: }
4827: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4828: ;
4829: };
4830: line[j+1]=0; /* Trims blanks at end of line */
4831: if(line[0]=='#'){
4832: fprintf(ficlog,"Comment line\n%s\n",line);
4833: printf("Comment line\n%s\n",line);
4834: continue;
4835: }
4836: trimbb(linetmp,line); /* Trims multiple blanks in line */
4837: for (j=0; line[j]!='\0';j++){
4838: line[j]=linetmp[j];
4839: }
4840:
4841:
4842: for (j=maxwav;j>=1;j--){
4843: cutv(stra, strb, line, ' ');
4844: if(strb[0]=='.') { /* Missing status */
4845: lval=-1;
4846: }else{
4847: errno=0;
4848: lval=strtol(strb,&endptr,10);
4849: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4850: if( strb[0]=='\0' || (*endptr != '\0')){
4851: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
4852: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
4853: return 1;
4854: }
4855: }
4856: s[j][i]=lval;
4857:
4858: strcpy(line,stra);
4859: cutv(stra, strb,line,' ');
4860: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4861: }
4862: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4863: month=99;
4864: year=9999;
4865: }else{
4866: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4867: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
4868: return 1;
4869: }
4870: anint[j][i]= (double) year;
4871: mint[j][i]= (double)month;
4872: strcpy(line,stra);
4873: } /* ENd Waves */
4874:
4875: cutv(stra, strb,line,' ');
4876: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4877: }
4878: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4879: month=99;
4880: year=9999;
4881: }else{
4882: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4883: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4884: return 1;
4885: }
4886: andc[i]=(double) year;
4887: moisdc[i]=(double) month;
4888: strcpy(line,stra);
4889:
4890: cutv(stra, strb,line,' ');
4891: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4892: }
4893: else if(iout=sscanf(strb,"%s.", dummy) != 0){
4894: month=99;
4895: year=9999;
4896: }else{
4897: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4898: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4899: return 1;
4900: }
4901: if (year==9999) {
4902: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
4903: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
4904: return 1;
4905:
4906: }
4907: annais[i]=(double)(year);
4908: moisnais[i]=(double)(month);
4909: strcpy(line,stra);
4910:
4911: cutv(stra, strb,line,' ');
4912: errno=0;
4913: dval=strtod(strb,&endptr);
4914: if( strb[0]=='\0' || (*endptr != '\0')){
4915: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4916: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4917: fflush(ficlog);
4918: return 1;
4919: }
4920: weight[i]=dval;
4921: strcpy(line,stra);
4922:
4923: for (j=ncovcol;j>=1;j--){
4924: cutv(stra, strb,line,' ');
4925: if(strb[0]=='.') { /* Missing status */
4926: lval=-1;
4927: }else{
4928: errno=0;
4929: lval=strtol(strb,&endptr,10);
4930: if( strb[0]=='\0' || (*endptr != '\0')){
4931: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
4932: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
4933: return 1;
4934: }
4935: }
4936: if(lval <-1 || lval >1){
4937: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4938: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4939: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4940: For example, for multinomial values like 1, 2 and 3,\n \
4941: build V1=0 V2=0 for the reference value (1),\n \
4942: V1=1 V2=0 for (2) \n \
4943: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4944: output of IMaCh is often meaningless.\n \
4945: Exiting.\n",lval,linei, i,line,j);
4946: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4947: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4948: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4949: For example, for multinomial values like 1, 2 and 3,\n \
4950: build V1=0 V2=0 for the reference value (1),\n \
4951: V1=1 V2=0 for (2) \n \
4952: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4953: output of IMaCh is often meaningless.\n \
4954: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4955: return 1;
4956: }
4957: covar[j][i]=(double)(lval);
4958: strcpy(line,stra);
4959: }
4960: lstra=strlen(stra);
4961:
4962: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4963: stratrunc = &(stra[lstra-9]);
4964: num[i]=atol(stratrunc);
4965: }
4966: else
4967: num[i]=atol(stra);
4968: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4969: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
4970:
4971: i=i+1;
4972: } /* End loop reading data */
4973:
4974: *imax=i-1; /* Number of individuals */
4975: fclose(fic);
4976:
4977: return (0);
4978: endread:
4979: printf("Exiting readdata: ");
4980: fclose(fic);
4981: return (1);
4982:
4983:
4984:
4985: }
4986: void removespace(char *str) {
4987: char *p1 = str, *p2 = str;
4988: do
4989: while (*p2 == ' ')
4990: p2++;
4991: while (*p1++ = *p2++);
4992: }
4993:
4994: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
4995: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
4996: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
4997: * - cptcovn or number of covariates k of the models excluding age*products =6
4998: * - cptcovage number of covariates with age*products =2
4999: * - cptcovs number of simple covariates
5000: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
5001: * which is a new column after the 9 (ncovcol) variables.
5002: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5003: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5004: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5005: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5006: */
5007: {
5008: int i, j, k, ks;
5009: int i1, j1, k1, k2;
5010: char modelsav[80];
5011: char stra[80], strb[80], strc[80], strd[80],stre[80];
5012:
5013: /*removespace(model);*/
5014: if (strlen(model) >1){ /* If there is at least 1 covariate */
5015: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5016: j=nbocc(model,'+'); /**< j=Number of '+' */
5017: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5018: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5019: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5020: /* including age products which are counted in cptcovage.
5021: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5022: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5023: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5024: strcpy(modelsav,model);
5025: if (strstr(model,"AGE") !=0){
5026: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5027: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5028: return 1;
5029: }
5030: if (strstr(model,"v") !=0){
5031: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5032: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5033: return 1;
5034: }
5035:
5036: /* Design
5037: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5038: * < ncovcol=8 >
5039: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5040: * k= 1 2 3 4 5 6 7 8
5041: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5042: * covar[k,i], value of kth covariate if not including age for individual i:
5043: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5044: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5045: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5046: * Tage[++cptcovage]=k
5047: * if products, new covar are created after ncovcol with k1
5048: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5049: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5050: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
5051: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5052: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5053: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5054: * < ncovcol=8 >
5055: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5056: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5057: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5058: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5059: * p Tprod[1]@2={ 6, 5}
5060: *p Tvard[1][1]@4= {7, 8, 5, 6}
5061: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5062: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5063: *How to reorganize?
5064: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5065: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5066: * {2, 1, 4, 8, 5, 6, 3, 7}
5067: * Struct []
5068: */
5069:
5070: /* This loop fills the array Tvar from the string 'model'.*/
5071: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5072: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5073: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5074: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5075: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5076: /* k=1 Tvar[1]=2 (from V2) */
5077: /* k=5 Tvar[5] */
5078: /* for (k=1; k<=cptcovn;k++) { */
5079: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5080: /* } */
5081: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5082: /*
5083: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5084: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5085: Tvar[k]=0;
5086: cptcovage=0;
5087: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5088: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5089: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5090: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5091: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5092: /*scanf("%d",i);*/
5093: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5094: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5095: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5096: /* covar is not filled and then is empty */
5097: cptcovprod--;
5098: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5099: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5100: cptcovage++; /* Sums the number of covariates which include age as a product */
5101: Tage[cptcovage]=k; /* Tage[1] = 4 */
5102: /*printf("stre=%s ", stre);*/
5103: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5104: cptcovprod--;
5105: cutl(stre,strb,strc,'V');
5106: Tvar[k]=atoi(stre);
5107: cptcovage++;
5108: Tage[cptcovage]=k;
5109: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5110: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5111: cptcovn++;
5112: cptcovprodnoage++;k1++;
5113: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5114: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5115: because this model-covariate is a construction we invent a new column
5116: ncovcol + k1
5117: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5118: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5119: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5120: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5121: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5122: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5123: k2=k2+2;
5124: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5125: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5126: for (i=1; i<=lastobs;i++){
5127: /* Computes the new covariate which is a product of
5128: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5129: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5130: }
5131: } /* End age is not in the model */
5132: } /* End if model includes a product */
5133: else { /* no more sum */
5134: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5135: /* scanf("%d",i);*/
5136: cutl(strd,strc,strb,'V');
5137: ks++; /**< Number of simple covariates */
5138: cptcovn++;
5139: Tvar[k]=atoi(strd);
5140: }
5141: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5142: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5143: scanf("%d",i);*/
5144: } /* end of loop + */
5145: } /* end model */
5146:
5147: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5148: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5149:
5150: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5151: printf("cptcovprod=%d ", cptcovprod);
5152: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5153:
5154: scanf("%d ",i);*/
5155:
5156:
5157: return (0); /* with covar[new additional covariate if product] and Tage if age */
5158: endread:
5159: printf("Exiting decodemodel: ");
5160: return (1);
5161: }
5162:
5163: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5164: {
5165: int i, m;
5166:
5167: for (i=1; i<=imx; i++) {
5168: for(m=2; (m<= maxwav); m++) {
5169: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5170: anint[m][i]=9999;
5171: s[m][i]=-1;
5172: }
5173: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5174: *nberr++;
5175: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
5176: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
5177: s[m][i]=-1;
5178: }
5179: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5180: *nberr++;
5181: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
5182: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
5183: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5184: }
5185: }
5186: }
5187:
5188: for (i=1; i<=imx; i++) {
5189: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5190: for(m=firstpass; (m<= lastpass); m++){
5191: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5192: if (s[m][i] >= nlstate+1) {
5193: if(agedc[i]>0)
5194: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5195: agev[m][i]=agedc[i];
5196: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5197: else {
5198: if ((int)andc[i]!=9999){
5199: nbwarn++;
5200: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5201: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5202: agev[m][i]=-1;
5203: }
5204: }
5205: }
5206: else if(s[m][i] !=9){ /* Standard case, age in fractional
5207: years but with the precision of a month */
5208: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5209: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5210: agev[m][i]=1;
5211: else if(agev[m][i] < *agemin){
5212: *agemin=agev[m][i];
5213: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5214: }
5215: else if(agev[m][i] >*agemax){
5216: *agemax=agev[m][i];
5217: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5218: }
5219: /*agev[m][i]=anint[m][i]-annais[i];*/
5220: /* agev[m][i] = age[i]+2*m;*/
5221: }
5222: else { /* =9 */
5223: agev[m][i]=1;
5224: s[m][i]=-1;
5225: }
5226: }
5227: else /*= 0 Unknown */
5228: agev[m][i]=1;
5229: }
5230:
5231: }
5232: for (i=1; i<=imx; i++) {
5233: for(m=firstpass; (m<=lastpass); m++){
5234: if (s[m][i] > (nlstate+ndeath)) {
5235: *nberr++;
5236: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
5237: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
5238: return 1;
5239: }
5240: }
5241: }
5242:
5243: /*for (i=1; i<=imx; i++){
5244: for (m=firstpass; (m<lastpass); m++){
5245: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5246: }
5247:
5248: }*/
5249:
5250:
5251: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5252: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5253:
5254: return (0);
5255: endread:
5256: printf("Exiting calandcheckages: ");
5257: return (1);
5258: }
5259:
5260:
5261: /***********************************************/
5262: /**************** Main Program *****************/
5263: /***********************************************/
5264:
5265: int main(int argc, char *argv[])
5266: {
5267: #ifdef GSL
5268: const gsl_multimin_fminimizer_type *T;
5269: size_t iteri = 0, it;
5270: int rval = GSL_CONTINUE;
5271: int status = GSL_SUCCESS;
5272: double ssval;
5273: #endif
5274: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5275: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5276: int linei, month, year,iout;
5277: int jj, ll, li, lj, lk, imk;
5278: int numlinepar=0; /* Current linenumber of parameter file */
5279: int itimes;
5280: int NDIM=2;
5281: int vpopbased=0;
5282:
5283: char ca[32], cb[32], cc[32];
5284: /* FILE *fichtm; *//* Html File */
5285: /* FILE *ficgp;*/ /*Gnuplot File */
5286: struct stat info;
5287: double agedeb, agefin,hf;
5288: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5289:
5290: double fret;
5291: double **xi,tmp,delta;
5292:
5293: double dum; /* Dummy variable */
5294: double ***p3mat;
5295: double ***mobaverage;
5296: int *indx;
5297: char line[MAXLINE], linepar[MAXLINE];
5298: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5299: char pathr[MAXLINE], pathimach[MAXLINE];
5300: char **bp, *tok, *val; /* pathtot */
5301: int firstobs=1, lastobs=10;
5302: int sdeb, sfin; /* Status at beginning and end */
5303: int c, h , cpt,l;
5304: int ju,jl, mi;
5305: int i1,j1, jk,aa,bb, stepsize, ij;
5306: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5307: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5308: int mobilav=0,popforecast=0;
5309: int hstepm, nhstepm;
5310: int agemortsup;
5311: float sumlpop=0.;
5312: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5313: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5314:
5315: double bage, fage, age, agelim, agebase;
5316: double ftolpl=FTOL;
5317: double **prlim;
5318: double ***param; /* Matrix of parameters */
5319: double *p;
5320: double **matcov; /* Matrix of covariance */
5321: double ***delti3; /* Scale */
5322: double *delti; /* Scale */
5323: double ***eij, ***vareij;
5324: double **varpl; /* Variances of prevalence limits by age */
5325: double *epj, vepp;
5326: double kk1, kk2;
5327: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5328: double **ximort;
5329: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5330: int *dcwave;
5331:
5332: char z[1]="c", occ;
5333:
5334: /*char *strt;*/
5335: char strtend[80];
5336:
5337: long total_usecs;
5338:
5339: /* setlocale (LC_ALL, ""); */
5340: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5341: /* textdomain (PACKAGE); */
5342: /* setlocale (LC_CTYPE, ""); */
5343: /* setlocale (LC_MESSAGES, ""); */
5344:
5345: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5346: rstart_time = time(NULL);
5347: /* (void) gettimeofday(&start_time,&tzp);*/
5348: start_time = *localtime(&rstart_time);
5349: curr_time=start_time;
5350: /*tml = *localtime(&start_time.tm_sec);*/
5351: /* strcpy(strstart,asctime(&tml)); */
5352: strcpy(strstart,asctime(&start_time));
5353:
5354: /* printf("Localtime (at start)=%s",strstart); */
5355: /* tp.tm_sec = tp.tm_sec +86400; */
5356: /* tm = *localtime(&start_time.tm_sec); */
5357: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5358: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5359: /* tmg.tm_hour=tmg.tm_hour + 1; */
5360: /* tp.tm_sec = mktime(&tmg); */
5361: /* strt=asctime(&tmg); */
5362: /* printf("Time(after) =%s",strstart); */
5363: /* (void) time (&time_value);
5364: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5365: * tm = *localtime(&time_value);
5366: * strstart=asctime(&tm);
5367: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5368: */
5369:
5370: nberr=0; /* Number of errors and warnings */
5371: nbwarn=0;
5372: getcwd(pathcd, size);
5373:
5374: printf("\n%s\n%s",version,fullversion);
5375: if(argc <=1){
5376: printf("\nEnter the parameter file name: ");
5377: fgets(pathr,FILENAMELENGTH,stdin);
5378: i=strlen(pathr);
5379: if(pathr[i-1]=='\n')
5380: pathr[i-1]='\0';
5381: i=strlen(pathr);
5382: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5383: pathr[i-1]='\0';
5384: for (tok = pathr; tok != NULL; ){
5385: printf("Pathr |%s|\n",pathr);
5386: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5387: printf("val= |%s| pathr=%s\n",val,pathr);
5388: strcpy (pathtot, val);
5389: if(pathr[0] == '\0') break; /* Dirty */
5390: }
5391: }
5392: else{
5393: strcpy(pathtot,argv[1]);
5394: }
5395: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5396: /*cygwin_split_path(pathtot,path,optionfile);
5397: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5398: /* cutv(path,optionfile,pathtot,'\\');*/
5399:
5400: /* Split argv[0], imach program to get pathimach */
5401: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5402: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5403: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5404: /* strcpy(pathimach,argv[0]); */
5405: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5406: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5407: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5408: chdir(path); /* Can be a relative path */
5409: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5410: printf("Current directory %s!\n",pathcd);
5411: strcpy(command,"mkdir ");
5412: strcat(command,optionfilefiname);
5413: if((outcmd=system(command)) != 0){
5414: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5415: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5416: /* fclose(ficlog); */
5417: /* exit(1); */
5418: }
5419: /* if((imk=mkdir(optionfilefiname))<0){ */
5420: /* perror("mkdir"); */
5421: /* } */
5422:
5423: /*-------- arguments in the command line --------*/
5424:
5425: /* Log file */
5426: strcat(filelog, optionfilefiname);
5427: strcat(filelog,".log"); /* */
5428: if((ficlog=fopen(filelog,"w"))==NULL) {
5429: printf("Problem with logfile %s\n",filelog);
5430: goto end;
5431: }
5432: fprintf(ficlog,"Log filename:%s\n",filelog);
5433: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5434: fprintf(ficlog,"\nEnter the parameter file name: \n");
5435: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5436: path=%s \n\
5437: optionfile=%s\n\
5438: optionfilext=%s\n\
5439: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5440:
5441: printf("Local time (at start):%s",strstart);
5442: fprintf(ficlog,"Local time (at start): %s",strstart);
5443: fflush(ficlog);
5444: /* (void) gettimeofday(&curr_time,&tzp); */
5445: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5446:
5447: /* */
5448: strcpy(fileres,"r");
5449: strcat(fileres, optionfilefiname);
5450: strcat(fileres,".txt"); /* Other files have txt extension */
5451:
5452: /*---------arguments file --------*/
5453:
5454: if((ficpar=fopen(optionfile,"r"))==NULL) {
5455: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5456: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5457: fflush(ficlog);
5458: /* goto end; */
5459: exit(70);
5460: }
5461:
5462:
5463:
5464: strcpy(filereso,"o");
5465: strcat(filereso,fileres);
5466: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5467: printf("Problem with Output resultfile: %s\n", filereso);
5468: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5469: fflush(ficlog);
5470: goto end;
5471: }
5472:
5473: /* Reads comments: lines beginning with '#' */
5474: numlinepar=0;
5475: while((c=getc(ficpar))=='#' && c!= EOF){
5476: ungetc(c,ficpar);
5477: fgets(line, MAXLINE, ficpar);
5478: numlinepar++;
5479: fputs(line,stdout);
5480: fputs(line,ficparo);
5481: fputs(line,ficlog);
5482: }
5483: ungetc(c,ficpar);
5484:
5485: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
5486: numlinepar++;
5487: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
5488: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5489: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
5490: fflush(ficlog);
5491: while((c=getc(ficpar))=='#' && c!= EOF){
5492: ungetc(c,ficpar);
5493: fgets(line, MAXLINE, ficpar);
5494: numlinepar++;
5495: fputs(line, stdout);
5496: //puts(line);
5497: fputs(line,ficparo);
5498: fputs(line,ficlog);
5499: }
5500: ungetc(c,ficpar);
5501:
5502:
5503: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5504: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5505: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5506: v1+v2*age+v2*v3 makes cptcovn = 3
5507: */
5508: if (strlen(model)>1)
5509: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5510: else
5511: ncovmodel=2;
5512: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5513: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5514: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5515: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5516: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
5517: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
5518: fflush(stdout);
5519: fclose (ficlog);
5520: goto end;
5521: }
5522: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5523: delti=delti3[1][1];
5524: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5525: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5526: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5527: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5528: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5529: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5530: fclose (ficparo);
5531: fclose (ficlog);
5532: goto end;
5533: exit(0);
5534: }
5535: else if(mle==-3) {
5536: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5537: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5538: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5539: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5540: matcov=matrix(1,npar,1,npar);
5541: }
5542: else{
5543: /* Read guessed parameters */
5544: /* Reads comments: lines beginning with '#' */
5545: while((c=getc(ficpar))=='#' && c!= EOF){
5546: ungetc(c,ficpar);
5547: fgets(line, MAXLINE, ficpar);
5548: numlinepar++;
5549: fputs(line,stdout);
5550: fputs(line,ficparo);
5551: fputs(line,ficlog);
5552: }
5553: ungetc(c,ficpar);
5554:
5555: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5556: for(i=1; i <=nlstate; i++){
5557: j=0;
5558: for(jj=1; jj <=nlstate+ndeath; jj++){
5559: if(jj==i) continue;
5560: j++;
5561: fscanf(ficpar,"%1d%1d",&i1,&j1);
5562: if ((i1 != i) && (j1 != j)){
5563: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5564: It might be a problem of design; if ncovcol and the model are correct\n \
5565: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5566: exit(1);
5567: }
5568: fprintf(ficparo,"%1d%1d",i1,j1);
5569: if(mle==1)
5570: printf("%1d%1d",i,j);
5571: fprintf(ficlog,"%1d%1d",i,j);
5572: for(k=1; k<=ncovmodel;k++){
5573: fscanf(ficpar," %lf",¶m[i][j][k]);
5574: if(mle==1){
5575: printf(" %lf",param[i][j][k]);
5576: fprintf(ficlog," %lf",param[i][j][k]);
5577: }
5578: else
5579: fprintf(ficlog," %lf",param[i][j][k]);
5580: fprintf(ficparo," %lf",param[i][j][k]);
5581: }
5582: fscanf(ficpar,"\n");
5583: numlinepar++;
5584: if(mle==1)
5585: printf("\n");
5586: fprintf(ficlog,"\n");
5587: fprintf(ficparo,"\n");
5588: }
5589: }
5590: fflush(ficlog);
5591:
5592: /* Reads scales values */
5593: p=param[1][1];
5594:
5595: /* Reads comments: lines beginning with '#' */
5596: while((c=getc(ficpar))=='#' && c!= EOF){
5597: ungetc(c,ficpar);
5598: fgets(line, MAXLINE, ficpar);
5599: numlinepar++;
5600: fputs(line,stdout);
5601: fputs(line,ficparo);
5602: fputs(line,ficlog);
5603: }
5604: ungetc(c,ficpar);
5605:
5606: for(i=1; i <=nlstate; i++){
5607: for(j=1; j <=nlstate+ndeath-1; j++){
5608: fscanf(ficpar,"%1d%1d",&i1,&j1);
5609: if ((i1-i)*(j1-j)!=0){
5610: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5611: exit(1);
5612: }
5613: printf("%1d%1d",i,j);
5614: fprintf(ficparo,"%1d%1d",i1,j1);
5615: fprintf(ficlog,"%1d%1d",i1,j1);
5616: for(k=1; k<=ncovmodel;k++){
5617: fscanf(ficpar,"%le",&delti3[i][j][k]);
5618: printf(" %le",delti3[i][j][k]);
5619: fprintf(ficparo," %le",delti3[i][j][k]);
5620: fprintf(ficlog," %le",delti3[i][j][k]);
5621: }
5622: fscanf(ficpar,"\n");
5623: numlinepar++;
5624: printf("\n");
5625: fprintf(ficparo,"\n");
5626: fprintf(ficlog,"\n");
5627: }
5628: }
5629: fflush(ficlog);
5630:
5631: /* Reads covariance matrix */
5632: delti=delti3[1][1];
5633:
5634:
5635: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5636:
5637: /* Reads comments: lines beginning with '#' */
5638: while((c=getc(ficpar))=='#' && c!= EOF){
5639: ungetc(c,ficpar);
5640: fgets(line, MAXLINE, ficpar);
5641: numlinepar++;
5642: fputs(line,stdout);
5643: fputs(line,ficparo);
5644: fputs(line,ficlog);
5645: }
5646: ungetc(c,ficpar);
5647:
5648: matcov=matrix(1,npar,1,npar);
5649: for(i=1; i <=npar; i++)
5650: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5651:
5652: for(i=1; i <=npar; i++){
5653: fscanf(ficpar,"%s",str);
5654: if(mle==1)
5655: printf("%s",str);
5656: fprintf(ficlog,"%s",str);
5657: fprintf(ficparo,"%s",str);
5658: for(j=1; j <=i; j++){
5659: fscanf(ficpar," %le",&matcov[i][j]);
5660: if(mle==1){
5661: printf(" %.5le",matcov[i][j]);
5662: }
5663: fprintf(ficlog," %.5le",matcov[i][j]);
5664: fprintf(ficparo," %.5le",matcov[i][j]);
5665: }
5666: fscanf(ficpar,"\n");
5667: numlinepar++;
5668: if(mle==1)
5669: printf("\n");
5670: fprintf(ficlog,"\n");
5671: fprintf(ficparo,"\n");
5672: }
5673: for(i=1; i <=npar; i++)
5674: for(j=i+1;j<=npar;j++)
5675: matcov[i][j]=matcov[j][i];
5676:
5677: if(mle==1)
5678: printf("\n");
5679: fprintf(ficlog,"\n");
5680:
5681: fflush(ficlog);
5682:
5683: /*-------- Rewriting parameter file ----------*/
5684: strcpy(rfileres,"r"); /* "Rparameterfile */
5685: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5686: strcat(rfileres,"."); /* */
5687: strcat(rfileres,optionfilext); /* Other files have txt extension */
5688: if((ficres =fopen(rfileres,"w"))==NULL) {
5689: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5690: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5691: }
5692: fprintf(ficres,"#%s\n",version);
5693: } /* End of mle != -3 */
5694:
5695:
5696: n= lastobs;
5697: num=lvector(1,n);
5698: moisnais=vector(1,n);
5699: annais=vector(1,n);
5700: moisdc=vector(1,n);
5701: andc=vector(1,n);
5702: agedc=vector(1,n);
5703: cod=ivector(1,n);
5704: weight=vector(1,n);
5705: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5706: mint=matrix(1,maxwav,1,n);
5707: anint=matrix(1,maxwav,1,n);
5708: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5709: tab=ivector(1,NCOVMAX);
5710: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5711:
5712: /* Reads data from file datafile */
5713: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5714: goto end;
5715:
5716: /* Calculation of the number of parameters from char model */
5717: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5718: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5719: k=3 V4 Tvar[k=3]= 4 (from V4)
5720: k=2 V1 Tvar[k=2]= 1 (from V1)
5721: k=1 Tvar[1]=2 (from V2)
5722: */
5723: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5724: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5725: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5726: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5727: */
5728: /* For model-covariate k tells which data-covariate to use but
5729: because this model-covariate is a construction we invent a new column
5730: ncovcol + k1
5731: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5732: Tvar[3=V1*V4]=4+1 etc */
5733: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5734: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5735: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5736: */
5737: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5738: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
5739: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5740: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5741: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5742: 4 covariates (3 plus signs)
5743: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5744: */
5745:
5746: if(decodemodel(model, lastobs) == 1)
5747: goto end;
5748:
5749: if((double)(lastobs-imx)/(double)imx > 1.10){
5750: nbwarn++;
5751: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5752: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5753: }
5754: /* if(mle==1){*/
5755: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5756: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5757: }
5758:
5759: /*-calculation of age at interview from date of interview and age at death -*/
5760: agev=matrix(1,maxwav,1,imx);
5761:
5762: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5763: goto end;
5764:
5765:
5766: agegomp=(int)agemin;
5767: free_vector(moisnais,1,n);
5768: free_vector(annais,1,n);
5769: /* free_matrix(mint,1,maxwav,1,n);
5770: free_matrix(anint,1,maxwav,1,n);*/
5771: free_vector(moisdc,1,n);
5772: free_vector(andc,1,n);
5773: /* */
5774:
5775: wav=ivector(1,imx);
5776: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5777: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5778: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5779:
5780: /* Concatenates waves */
5781: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5782: /* */
5783:
5784: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5785:
5786: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5787: ncodemax[1]=1;
5788: Ndum =ivector(-1,NCOVMAX);
5789: if (ncovmodel > 2)
5790: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5791:
5792: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5793: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5794: h=0;
5795:
5796:
5797: /*if (cptcovn > 0) */
5798:
5799:
5800: m=pow(2,cptcoveff);
5801:
5802: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5803: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5804: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5805: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5806: h++;
5807: if (h>m)
5808: h=1;
5809: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5810: * h 1 2 3 4
5811: *______________________________
5812: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5813: * 2 2 1 1 1
5814: * 3 i=2 1 2 1 1
5815: * 4 2 2 1 1
5816: * 5 i=3 1 i=2 1 2 1
5817: * 6 2 1 2 1
5818: * 7 i=4 1 2 2 1
5819: * 8 2 2 2 1
5820: * 9 i=5 1 i=3 1 i=2 1 1
5821: * 10 2 1 1 1
5822: * 11 i=6 1 2 1 1
5823: * 12 2 2 1 1
5824: * 13 i=7 1 i=4 1 2 1
5825: * 14 2 1 2 1
5826: * 15 i=8 1 2 2 1
5827: * 16 2 2 2 1
5828: */
5829: codtab[h][k]=j;
5830: /*codtab[h][Tvar[k]]=j;*/
5831: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
5832: }
5833: }
5834: }
5835: }
5836: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5837: codtab[1][2]=1;codtab[2][2]=2; */
5838: /* for(i=1; i <=m ;i++){
5839: for(k=1; k <=cptcovn; k++){
5840: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5841: }
5842: printf("\n");
5843: }
5844: scanf("%d",i);*/
5845:
5846: free_ivector(Ndum,-1,NCOVMAX);
5847:
5848:
5849:
5850: /*------------ gnuplot -------------*/
5851: strcpy(optionfilegnuplot,optionfilefiname);
5852: if(mle==-3)
5853: strcat(optionfilegnuplot,"-mort");
5854: strcat(optionfilegnuplot,".gp");
5855:
5856: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5857: printf("Problem with file %s",optionfilegnuplot);
5858: }
5859: else{
5860: fprintf(ficgp,"\n# %s\n", version);
5861: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5862: //fprintf(ficgp,"set missing 'NaNq'\n");
5863: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5864: }
5865: /* fclose(ficgp);*/
5866: /*--------- index.htm --------*/
5867:
5868: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5869: if(mle==-3)
5870: strcat(optionfilehtm,"-mort");
5871: strcat(optionfilehtm,".htm");
5872: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5873: printf("Problem with %s \n",optionfilehtm);
5874: exit(0);
5875: }
5876:
5877: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5878: strcat(optionfilehtmcov,"-cov.htm");
5879: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5880: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5881: }
5882: else{
5883: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5884: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5885: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5886: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5887: }
5888:
5889: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5890: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5891: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5892: \n\
5893: <hr size=\"2\" color=\"#EC5E5E\">\
5894: <ul><li><h4>Parameter files</h4>\n\
5895: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5896: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5897: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5898: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5899: - Date and time at start: %s</ul>\n",\
5900: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5901: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5902: fileres,fileres,\
5903: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5904: fflush(fichtm);
5905:
5906: strcpy(pathr,path);
5907: strcat(pathr,optionfilefiname);
5908: chdir(optionfilefiname); /* Move to directory named optionfile */
5909:
5910: /* Calculates basic frequencies. Computes observed prevalence at single age
5911: and prints on file fileres'p'. */
5912: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5913:
5914: fprintf(fichtm,"\n");
5915: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5916: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5917: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5918: imx,agemin,agemax,jmin,jmax,jmean);
5919: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5920: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5921: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5922: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5923: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5924:
5925:
5926: /* For Powell, parameters are in a vector p[] starting at p[1]
5927: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5928: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5929:
5930: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5931:
5932: if (mle==-3){
5933: ximort=matrix(1,NDIM,1,NDIM);
5934: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5935: cens=ivector(1,n);
5936: ageexmed=vector(1,n);
5937: agecens=vector(1,n);
5938: dcwave=ivector(1,n);
5939:
5940: for (i=1; i<=imx; i++){
5941: dcwave[i]=-1;
5942: for (m=firstpass; m<=lastpass; m++)
5943: if (s[m][i]>nlstate) {
5944: dcwave[i]=m;
5945: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5946: break;
5947: }
5948: }
5949:
5950: for (i=1; i<=imx; i++) {
5951: if (wav[i]>0){
5952: ageexmed[i]=agev[mw[1][i]][i];
5953: j=wav[i];
5954: agecens[i]=1.;
5955:
5956: if (ageexmed[i]> 1 && wav[i] > 0){
5957: agecens[i]=agev[mw[j][i]][i];
5958: cens[i]= 1;
5959: }else if (ageexmed[i]< 1)
5960: cens[i]= -1;
5961: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5962: cens[i]=0 ;
5963: }
5964: else cens[i]=-1;
5965: }
5966:
5967: for (i=1;i<=NDIM;i++) {
5968: for (j=1;j<=NDIM;j++)
5969: ximort[i][j]=(i == j ? 1.0 : 0.0);
5970: }
5971:
5972: /*p[1]=0.0268; p[NDIM]=0.083;*/
5973: /*printf("%lf %lf", p[1], p[2]);*/
5974:
5975:
5976: #ifdef GSL
5977: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5978: #elsedef
5979: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5980: #endif
5981: strcpy(filerespow,"pow-mort");
5982: strcat(filerespow,fileres);
5983: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5984: printf("Problem with resultfile: %s\n", filerespow);
5985: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5986: }
5987: #ifdef GSL
5988: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5989: #elsedef
5990: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5991: #endif
5992: /* for (i=1;i<=nlstate;i++)
5993: for(j=1;j<=nlstate+ndeath;j++)
5994: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5995: */
5996: fprintf(ficrespow,"\n");
5997: #ifdef GSL
5998: /* gsl starts here */
5999: T = gsl_multimin_fminimizer_nmsimplex;
6000: gsl_multimin_fminimizer *sfm = NULL;
6001: gsl_vector *ss, *x;
6002: gsl_multimin_function minex_func;
6003:
6004: /* Initial vertex size vector */
6005: ss = gsl_vector_alloc (NDIM);
6006:
6007: if (ss == NULL){
6008: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6009: }
6010: /* Set all step sizes to 1 */
6011: gsl_vector_set_all (ss, 0.001);
6012:
6013: /* Starting point */
6014:
6015: x = gsl_vector_alloc (NDIM);
6016:
6017: if (x == NULL){
6018: gsl_vector_free(ss);
6019: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6020: }
6021:
6022: /* Initialize method and iterate */
6023: /* p[1]=0.0268; p[NDIM]=0.083; */
6024: /* gsl_vector_set(x, 0, 0.0268); */
6025: /* gsl_vector_set(x, 1, 0.083); */
6026: gsl_vector_set(x, 0, p[1]);
6027: gsl_vector_set(x, 1, p[2]);
6028:
6029: minex_func.f = &gompertz_f;
6030: minex_func.n = NDIM;
6031: minex_func.params = (void *)&p; /* ??? */
6032:
6033: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6034: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6035:
6036: printf("Iterations beginning .....\n\n");
6037: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6038:
6039: iteri=0;
6040: while (rval == GSL_CONTINUE){
6041: iteri++;
6042: status = gsl_multimin_fminimizer_iterate(sfm);
6043:
6044: if (status) printf("error: %s\n", gsl_strerror (status));
6045: fflush(0);
6046:
6047: if (status)
6048: break;
6049:
6050: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6051: ssval = gsl_multimin_fminimizer_size (sfm);
6052:
6053: if (rval == GSL_SUCCESS)
6054: printf ("converged to a local maximum at\n");
6055:
6056: printf("%5d ", iteri);
6057: for (it = 0; it < NDIM; it++){
6058: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6059: }
6060: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6061: }
6062:
6063: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6064:
6065: gsl_vector_free(x); /* initial values */
6066: gsl_vector_free(ss); /* inital step size */
6067: for (it=0; it<NDIM; it++){
6068: p[it+1]=gsl_vector_get(sfm->x,it);
6069: fprintf(ficrespow," %.12lf", p[it]);
6070: }
6071: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6072: #endif
6073: #ifdef POWELL
6074: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6075: #endif
6076: fclose(ficrespow);
6077:
6078: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6079:
6080: for(i=1; i <=NDIM; i++)
6081: for(j=i+1;j<=NDIM;j++)
6082: matcov[i][j]=matcov[j][i];
6083:
6084: printf("\nCovariance matrix\n ");
6085: for(i=1; i <=NDIM; i++) {
6086: for(j=1;j<=NDIM;j++){
6087: printf("%f ",matcov[i][j]);
6088: }
6089: printf("\n ");
6090: }
6091:
6092: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6093: for (i=1;i<=NDIM;i++)
6094: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6095:
6096: lsurv=vector(1,AGESUP);
6097: lpop=vector(1,AGESUP);
6098: tpop=vector(1,AGESUP);
6099: lsurv[agegomp]=100000;
6100:
6101: for (k=agegomp;k<=AGESUP;k++) {
6102: agemortsup=k;
6103: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6104: }
6105:
6106: for (k=agegomp;k<agemortsup;k++)
6107: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6108:
6109: for (k=agegomp;k<agemortsup;k++){
6110: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6111: sumlpop=sumlpop+lpop[k];
6112: }
6113:
6114: tpop[agegomp]=sumlpop;
6115: for (k=agegomp;k<(agemortsup-3);k++){
6116: /* tpop[k+1]=2;*/
6117: tpop[k+1]=tpop[k]-lpop[k];
6118: }
6119:
6120:
6121: printf("\nAge lx qx dx Lx Tx e(x)\n");
6122: for (k=agegomp;k<(agemortsup-2);k++)
6123: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
6124:
6125:
6126: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6127: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6128:
6129: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6130: stepm, weightopt,\
6131: model,imx,p,matcov,agemortsup);
6132:
6133: free_vector(lsurv,1,AGESUP);
6134: free_vector(lpop,1,AGESUP);
6135: free_vector(tpop,1,AGESUP);
6136: #ifdef GSL
6137: free_ivector(cens,1,n);
6138: free_vector(agecens,1,n);
6139: free_ivector(dcwave,1,n);
6140: free_matrix(ximort,1,NDIM,1,NDIM);
6141: #endif
6142: } /* Endof if mle==-3 */
6143:
6144: else{ /* For mle >=1 */
6145: globpr=0;/* debug */
6146: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6147: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6148: for (k=1; k<=npar;k++)
6149: printf(" %d %8.5f",k,p[k]);
6150: printf("\n");
6151: globpr=1; /* to print the contributions */
6152: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6153: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6154: for (k=1; k<=npar;k++)
6155: printf(" %d %8.5f",k,p[k]);
6156: printf("\n");
6157: if(mle>=1){ /* Could be 1 or 2 */
6158: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6159: }
6160:
6161: /*--------- results files --------------*/
6162: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
6163:
6164:
6165: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6166: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6167: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6168: for(i=1,jk=1; i <=nlstate; i++){
6169: for(k=1; k <=(nlstate+ndeath); k++){
6170: if (k != i) {
6171: printf("%d%d ",i,k);
6172: fprintf(ficlog,"%d%d ",i,k);
6173: fprintf(ficres,"%1d%1d ",i,k);
6174: for(j=1; j <=ncovmodel; j++){
6175: printf("%lf ",p[jk]);
6176: fprintf(ficlog,"%lf ",p[jk]);
6177: fprintf(ficres,"%lf ",p[jk]);
6178: jk++;
6179: }
6180: printf("\n");
6181: fprintf(ficlog,"\n");
6182: fprintf(ficres,"\n");
6183: }
6184: }
6185: }
6186: if(mle!=0){
6187: /* Computing hessian and covariance matrix */
6188: ftolhess=ftol; /* Usually correct */
6189: hesscov(matcov, p, npar, delti, ftolhess, func);
6190: }
6191: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6192: printf("# Scales (for hessian or gradient estimation)\n");
6193: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6194: for(i=1,jk=1; i <=nlstate; i++){
6195: for(j=1; j <=nlstate+ndeath; j++){
6196: if (j!=i) {
6197: fprintf(ficres,"%1d%1d",i,j);
6198: printf("%1d%1d",i,j);
6199: fprintf(ficlog,"%1d%1d",i,j);
6200: for(k=1; k<=ncovmodel;k++){
6201: printf(" %.5e",delti[jk]);
6202: fprintf(ficlog," %.5e",delti[jk]);
6203: fprintf(ficres," %.5e",delti[jk]);
6204: jk++;
6205: }
6206: printf("\n");
6207: fprintf(ficlog,"\n");
6208: fprintf(ficres,"\n");
6209: }
6210: }
6211: }
6212:
6213: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
6214: if(mle>=1)
6215: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
6216: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
6217: /* # 121 Var(a12)\n\ */
6218: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6219: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6220: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6221: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6222: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6223: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6224: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6225:
6226:
6227: /* Just to have a covariance matrix which will be more understandable
6228: even is we still don't want to manage dictionary of variables
6229: */
6230: for(itimes=1;itimes<=2;itimes++){
6231: jj=0;
6232: for(i=1; i <=nlstate; i++){
6233: for(j=1; j <=nlstate+ndeath; j++){
6234: if(j==i) continue;
6235: for(k=1; k<=ncovmodel;k++){
6236: jj++;
6237: ca[0]= k+'a'-1;ca[1]='\0';
6238: if(itimes==1){
6239: if(mle>=1)
6240: printf("#%1d%1d%d",i,j,k);
6241: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6242: fprintf(ficres,"#%1d%1d%d",i,j,k);
6243: }else{
6244: if(mle>=1)
6245: printf("%1d%1d%d",i,j,k);
6246: fprintf(ficlog,"%1d%1d%d",i,j,k);
6247: fprintf(ficres,"%1d%1d%d",i,j,k);
6248: }
6249: ll=0;
6250: for(li=1;li <=nlstate; li++){
6251: for(lj=1;lj <=nlstate+ndeath; lj++){
6252: if(lj==li) continue;
6253: for(lk=1;lk<=ncovmodel;lk++){
6254: ll++;
6255: if(ll<=jj){
6256: cb[0]= lk +'a'-1;cb[1]='\0';
6257: if(ll<jj){
6258: if(itimes==1){
6259: if(mle>=1)
6260: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6261: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6262: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6263: }else{
6264: if(mle>=1)
6265: printf(" %.5e",matcov[jj][ll]);
6266: fprintf(ficlog," %.5e",matcov[jj][ll]);
6267: fprintf(ficres," %.5e",matcov[jj][ll]);
6268: }
6269: }else{
6270: if(itimes==1){
6271: if(mle>=1)
6272: printf(" Var(%s%1d%1d)",ca,i,j);
6273: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6274: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6275: }else{
6276: if(mle>=1)
6277: printf(" %.5e",matcov[jj][ll]);
6278: fprintf(ficlog," %.5e",matcov[jj][ll]);
6279: fprintf(ficres," %.5e",matcov[jj][ll]);
6280: }
6281: }
6282: }
6283: } /* end lk */
6284: } /* end lj */
6285: } /* end li */
6286: if(mle>=1)
6287: printf("\n");
6288: fprintf(ficlog,"\n");
6289: fprintf(ficres,"\n");
6290: numlinepar++;
6291: } /* end k*/
6292: } /*end j */
6293: } /* end i */
6294: } /* end itimes */
6295:
6296: fflush(ficlog);
6297: fflush(ficres);
6298:
6299: while((c=getc(ficpar))=='#' && c!= EOF){
6300: ungetc(c,ficpar);
6301: fgets(line, MAXLINE, ficpar);
6302: fputs(line,stdout);
6303: fputs(line,ficparo);
6304: }
6305: ungetc(c,ficpar);
6306:
6307: estepm=0;
6308: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6309: if (estepm==0 || estepm < stepm) estepm=stepm;
6310: if (fage <= 2) {
6311: bage = ageminpar;
6312: fage = agemaxpar;
6313: }
6314:
6315: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6316: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6317: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6318:
6319: while((c=getc(ficpar))=='#' && c!= EOF){
6320: ungetc(c,ficpar);
6321: fgets(line, MAXLINE, ficpar);
6322: fputs(line,stdout);
6323: fputs(line,ficparo);
6324: }
6325: ungetc(c,ficpar);
6326:
6327: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
6328: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6329: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6330: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6331: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6332:
6333: while((c=getc(ficpar))=='#' && c!= EOF){
6334: ungetc(c,ficpar);
6335: fgets(line, MAXLINE, ficpar);
6336: fputs(line,stdout);
6337: fputs(line,ficparo);
6338: }
6339: ungetc(c,ficpar);
6340:
6341:
6342: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6343: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6344:
6345: fscanf(ficpar,"pop_based=%d\n",&popbased);
6346: fprintf(ficparo,"pop_based=%d\n",popbased);
6347: fprintf(ficres,"pop_based=%d\n",popbased);
6348:
6349: while((c=getc(ficpar))=='#' && c!= EOF){
6350: ungetc(c,ficpar);
6351: fgets(line, MAXLINE, ficpar);
6352: fputs(line,stdout);
6353: fputs(line,ficparo);
6354: }
6355: ungetc(c,ficpar);
6356:
6357: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
6358: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
6359: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
6360: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
6361: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
6362: /* day and month of proj2 are not used but only year anproj2.*/
6363:
6364:
6365:
6366: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6367: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6368:
6369: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6370: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6371:
6372: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6373: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6374: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6375:
6376: /*------------ free_vector -------------*/
6377: /* chdir(path); */
6378:
6379: free_ivector(wav,1,imx);
6380: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6381: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6382: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6383: free_lvector(num,1,n);
6384: free_vector(agedc,1,n);
6385: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6386: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6387: fclose(ficparo);
6388: fclose(ficres);
6389:
6390:
6391: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6392: #include "prevlim.h" /* Use ficrespl, ficlog */
6393: fclose(ficrespl);
6394:
6395: #ifdef FREEEXIT2
6396: #include "freeexit2.h"
6397: #endif
6398:
6399: /*------------- h Pij x at various ages ------------*/
6400: #include "hpijx.h"
6401: fclose(ficrespij);
6402:
6403: /*-------------- Variance of one-step probabilities---*/
6404: k=1;
6405: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6406:
6407:
6408: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6409: for(i=1;i<=AGESUP;i++)
6410: for(j=1;j<=NCOVMAX;j++)
6411: for(k=1;k<=NCOVMAX;k++)
6412: probs[i][j][k]=0.;
6413:
6414: /*---------- Forecasting ------------------*/
6415: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6416: if(prevfcast==1){
6417: /* if(stepm ==1){*/
6418: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6419: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6420: /* } */
6421: /* else{ */
6422: /* erreur=108; */
6423: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
6424: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
6425: /* } */
6426: }
6427:
6428:
6429: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6430:
6431: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6432: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
6433: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6434: */
6435:
6436: if (mobilav!=0) {
6437: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6438: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6439: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6440: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6441: }
6442: }
6443:
6444:
6445: /*---------- Health expectancies, no variances ------------*/
6446:
6447: strcpy(filerese,"e");
6448: strcat(filerese,fileres);
6449: if((ficreseij=fopen(filerese,"w"))==NULL) {
6450: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6451: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6452: }
6453: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6454: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6455: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6456: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6457:
6458: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6459: fprintf(ficreseij,"\n#****** ");
6460: for(j=1;j<=cptcoveff;j++) {
6461: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6462: }
6463: fprintf(ficreseij,"******\n");
6464:
6465: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6466: oldm=oldms;savm=savms;
6467: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6468:
6469: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6470: /*}*/
6471: }
6472: fclose(ficreseij);
6473:
6474:
6475: /*---------- Health expectancies and variances ------------*/
6476:
6477:
6478: strcpy(filerest,"t");
6479: strcat(filerest,fileres);
6480: if((ficrest=fopen(filerest,"w"))==NULL) {
6481: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6482: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6483: }
6484: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6485: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6486:
6487:
6488: strcpy(fileresstde,"stde");
6489: strcat(fileresstde,fileres);
6490: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6491: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6492: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6493: }
6494: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6495: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6496:
6497: strcpy(filerescve,"cve");
6498: strcat(filerescve,fileres);
6499: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6500: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6501: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6502: }
6503: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6504: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6505:
6506: strcpy(fileresv,"v");
6507: strcat(fileresv,fileres);
6508: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6509: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6510: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6511: }
6512: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6513: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6514:
6515: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6516: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6517:
6518: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6519: fprintf(ficrest,"\n#****** ");
6520: for(j=1;j<=cptcoveff;j++)
6521: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6522: fprintf(ficrest,"******\n");
6523:
6524: fprintf(ficresstdeij,"\n#****** ");
6525: fprintf(ficrescveij,"\n#****** ");
6526: for(j=1;j<=cptcoveff;j++) {
6527: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6528: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6529: }
6530: fprintf(ficresstdeij,"******\n");
6531: fprintf(ficrescveij,"******\n");
6532:
6533: fprintf(ficresvij,"\n#****** ");
6534: for(j=1;j<=cptcoveff;j++)
6535: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6536: fprintf(ficresvij,"******\n");
6537:
6538: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6539: oldm=oldms;savm=savms;
6540: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6541: /*
6542: */
6543: /* goto endfree; */
6544:
6545: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6546: pstamp(ficrest);
6547:
6548:
6549: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6550: oldm=oldms;savm=savms; /* Segmentation fault */
6551: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6552: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
6553: if(vpopbased==1)
6554: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
6555: else
6556: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6557: fprintf(ficrest,"# Age e.. (std) ");
6558: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6559: fprintf(ficrest,"\n");
6560:
6561: epj=vector(1,nlstate+1);
6562: for(age=bage; age <=fage ;age++){
6563: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6564: if (vpopbased==1) {
6565: if(mobilav ==0){
6566: for(i=1; i<=nlstate;i++)
6567: prlim[i][i]=probs[(int)age][i][k];
6568: }else{ /* mobilav */
6569: for(i=1; i<=nlstate;i++)
6570: prlim[i][i]=mobaverage[(int)age][i][k];
6571: }
6572: }
6573:
6574: fprintf(ficrest," %4.0f",age);
6575: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6576: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6577: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6578: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6579: }
6580: epj[nlstate+1] +=epj[j];
6581: }
6582:
6583: for(i=1, vepp=0.;i <=nlstate;i++)
6584: for(j=1;j <=nlstate;j++)
6585: vepp += vareij[i][j][(int)age];
6586: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6587: for(j=1;j <=nlstate;j++){
6588: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6589: }
6590: fprintf(ficrest,"\n");
6591: }
6592: }
6593: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6594: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6595: free_vector(epj,1,nlstate+1);
6596: /*}*/
6597: }
6598: free_vector(weight,1,n);
6599: free_imatrix(Tvard,1,NCOVMAX,1,2);
6600: free_imatrix(s,1,maxwav+1,1,n);
6601: free_matrix(anint,1,maxwav,1,n);
6602: free_matrix(mint,1,maxwav,1,n);
6603: free_ivector(cod,1,n);
6604: free_ivector(tab,1,NCOVMAX);
6605: fclose(ficresstdeij);
6606: fclose(ficrescveij);
6607: fclose(ficresvij);
6608: fclose(ficrest);
6609: fclose(ficpar);
6610:
6611: /*------- Variance of period (stable) prevalence------*/
6612:
6613: strcpy(fileresvpl,"vpl");
6614: strcat(fileresvpl,fileres);
6615: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6616: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6617: exit(0);
6618: }
6619: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6620:
6621: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6622: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6623:
6624: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6625: fprintf(ficresvpl,"\n#****** ");
6626: for(j=1;j<=cptcoveff;j++)
6627: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6628: fprintf(ficresvpl,"******\n");
6629:
6630: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6631: oldm=oldms;savm=savms;
6632: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6633: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6634: /*}*/
6635: }
6636:
6637: fclose(ficresvpl);
6638:
6639: /*---------- End : free ----------------*/
6640: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6641: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6642: } /* mle==-3 arrives here for freeing */
6643: endfree:
6644: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6645: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6646: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6647: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6648: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6649: free_matrix(covar,0,NCOVMAX,1,n);
6650: free_matrix(matcov,1,npar,1,npar);
6651: /*free_vector(delti,1,npar);*/
6652: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6653: free_matrix(agev,1,maxwav,1,imx);
6654: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6655:
6656: free_ivector(ncodemax,1,NCOVMAX);
6657: free_ivector(Tvar,1,NCOVMAX);
6658: free_ivector(Tprod,1,NCOVMAX);
6659: free_ivector(Tvaraff,1,NCOVMAX);
6660: free_ivector(Tage,1,NCOVMAX);
6661:
6662: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6663: free_imatrix(codtab,1,100,1,10);
6664: fflush(fichtm);
6665: fflush(ficgp);
6666:
6667:
6668: if((nberr >0) || (nbwarn>0)){
6669: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6670: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6671: }else{
6672: printf("End of Imach\n");
6673: fprintf(ficlog,"End of Imach\n");
6674: }
6675: printf("See log file on %s\n",filelog);
6676: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6677: /*(void) gettimeofday(&end_time,&tzp);*/
6678: rend_time = time(NULL);
6679: end_time = *localtime(&rend_time);
6680: /* tml = *localtime(&end_time.tm_sec); */
6681: strcpy(strtend,asctime(&end_time));
6682: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6683: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6684: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6685:
6686: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6687: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6688: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6689: /* printf("Total time was %d uSec.\n", total_usecs);*/
6690: /* if(fileappend(fichtm,optionfilehtm)){ */
6691: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6692: fclose(fichtm);
6693: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6694: fclose(fichtmcov);
6695: fclose(ficgp);
6696: fclose(ficlog);
6697: /*------ End -----------*/
6698:
6699:
6700: printf("Before Current directory %s!\n",pathcd);
6701: if(chdir(pathcd) != 0)
6702: printf("Can't move to directory %s!\n",path);
6703: if(getcwd(pathcd,MAXLINE) > 0)
6704: printf("Current directory %s!\n",pathcd);
6705: /*strcat(plotcmd,CHARSEPARATOR);*/
6706: sprintf(plotcmd,"gnuplot");
6707: #ifdef _WIN32
6708: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6709: #endif
6710: if(!stat(plotcmd,&info)){
6711: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6712: if(!stat(getenv("GNUPLOTBIN"),&info)){
6713: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6714: }else
6715: strcpy(pplotcmd,plotcmd);
6716: #ifdef __unix
6717: strcpy(plotcmd,GNUPLOTPROGRAM);
6718: if(!stat(plotcmd,&info)){
6719: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6720: }else
6721: strcpy(pplotcmd,plotcmd);
6722: #endif
6723: }else
6724: strcpy(pplotcmd,plotcmd);
6725:
6726: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6727: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6728:
6729: if((outcmd=system(plotcmd)) != 0){
6730: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6731: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6732: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6733: if((outcmd=system(plotcmd)) != 0)
6734: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6735: }
6736: printf(" Successful, please wait...");
6737: while (z[0] != 'q') {
6738: /* chdir(path); */
6739: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6740: scanf("%s",z);
6741: /* if (z[0] == 'c') system("./imach"); */
6742: if (z[0] == 'e') {
6743: #ifdef __APPLE__
6744: sprintf(pplotcmd, "open %s", optionfilehtm);
6745: #elif __linux
6746: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6747: #else
6748: sprintf(pplotcmd, "%s", optionfilehtm);
6749: #endif
6750: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6751: system(pplotcmd);
6752: }
6753: else if (z[0] == 'g') system(plotcmd);
6754: else if (z[0] == 'q') exit(0);
6755: }
6756: end:
6757: while (z[0] != 'q') {
6758: printf("\nType q for exiting: ");
6759: scanf("%s",z);
6760: }
6761: }
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